Package: SWATH2stats

Version: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2019-10-16 07:16:12 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:19:21 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 188.2 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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-3.9-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/3.6/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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
 23.892   2.758  27.331 

name	user	system	elapsed
JPP_update	0.195	0.014	0.208
add_genesymbol	0.015	0.000	0.014
assess_decoy_rate	0.178	0.011	0.189
assess_fdr_byrun	0.285	0.030	0.316
assess_fdr_overall	0.267	0.025	0.293
convert4MSstats	0.807	0.055	0.863
convert4PECA	0.222	0.011	0.234
convert4aLFQ	0.955	0.059	1.015
convert4mapDIA	0.730	0.059	0.790
convert4pythonscript	0.239	0.011	0.250
convert_protein_ids	1.073	0.076	3.283
count_analytes	0.196	0.007	0.203
disaggregate	0.711	0.075	0.785
filter_all_peptides	0.227	0.008	0.235
filter_mscore_all	0.369	0.096	0.290
filter_mscore_fdr	1.226	0.471	0.977
filter_on_max_peptides	0.461	0.170	0.318
filter_on_min_peptides	0.884	0.657	0.323
filter_proteotypic_peptides	1.262	0.075	0.276
import_data	0.723	0.061	0.784
load_mart	0.468	0.022	2.016
mscore4assayfdr	0.613	0.054	0.672
mscore4pepfdr	0.553	0.077	0.631
mscore4protfdr	0.458	0.009	0.471
plot.fdr_cube	0.195	0.005	0.200
plot.fdr_table	0.277	0.016	0.293
plot_correlation_between_samples	1.058	0.040	1.098
plot_variation	0.830	0.062	0.894
plot_variation_vs_total	0.686	0.065	0.751
reduce_OpenSWATH_output	0.205	0.002	0.208
removeDecoyProteins	0.224	0.003	0.228
sample_annotation	0.230	0.003	0.232
transform_MSstats_OpenSWATH	0.007	0.001	0.007
unifyProteinGroupLabels	0.159	0.007	0.166
write_matrix_peptides	0.191	0.018	0.208
write_matrix_proteins	0.179	0.012	0.192