Package: SWATH2stats

Version: 1.10.2

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_1.10.2.tar.gz

StartedAt: 2018-10-17 00:20:58 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:22:04 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 65.9 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_1.10.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.2’
* 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
* 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-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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: 118 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.872   1.385  11.533 

name	user	system	elapsed
assess_decoy_rate	0.179	0.008	0.189
assess_fdr_byrun	0.210	0.019	0.231
assess_fdr_overall	0.265	0.024	0.292
convert4MSstats	0.660	0.027	0.697
convert4PECA	0.244	0.004	0.251
convert4aLFQ	0.707	0.037	0.751
convert4mapDIA	0.854	0.035	0.901
convert4pythonscript	0.188	0.004	0.195
count_analytes	0.185	0.007	0.194
disaggregate	0.508	0.019	0.532
filter_all_peptides	0.229	0.005	0.235
filter_mscore_all	0.348	0.006	0.285
filter_mscore_fdr	0.900	0.090	0.691
filter_on_max_peptides	0.312	0.092	0.252
filter_on_min_peptides	0.684	0.557	0.262
filter_proteotypic_peptides	0.556	0.471	0.202
import_data	0.747	0.032	0.799
mscore4assayfdr	0.463	0.020	0.491
mscore4pepfdr	0.407	0.012	0.427
mscore4protfdr	0.337	0.012	0.359
plot.fdr_cube	0.170	0.002	0.175
plot.fdr_table	0.219	0.005	0.230
plot_correlation_between_samples	0.802	0.007	0.821
plot_variation	0.713	0.026	0.749
plot_variation_vs_total	0.844	0.025	0.882
reduce_OpenSWATH_output	0.179	0.002	0.184
removeDecoyProteins	0.184	0.002	0.187
sample_annotation	0.189	0.002	0.195
transform_MSstats_OpenSWATH	0.010	0.001	0.010
unifyProteinGroupLabels	0.186	0.002	0.193
write_matrix_peptides	0.192	0.008	0.207
write_matrix_proteins	0.168	0.002	0.174