Package: SWATH2stats

Version: 1.13.5

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_1.13.5.tar.gz

StartedAt: 2019-04-09 04:02:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:05:32 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 198.2 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_1.13.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.13.5’
* 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 0.488  0.044  23.028
load_mart           0.391  0.015  25.147
* 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’ ...
** 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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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: 120 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.147   3.830  36.504 

name	user	system	elapsed
JPP_update	0.140	0.007	0.151
add_genesymbol	0.012	0.001	0.015
assess_decoy_rate	0.120	0.004	0.125
assess_fdr_byrun	0.228	0.013	0.261
assess_fdr_overall	0.198	0.008	0.206
convert4MSstats	0.719	0.025	0.744
convert4PECA	0.183	0.007	0.190
convert4aLFQ	0.748	0.025	0.815
convert4mapDIA	0.619	0.028	0.652
convert4pythonscript	0.162	0.006	0.171
convert_protein_ids	0.488	0.044	23.028
count_analytes	0.189	0.005	0.194
disaggregate	0.485	0.031	0.517
filter_all_peptides	0.160	0.006	0.203
filter_mscore_all	0.385	0.286	0.234
filter_mscore_fdr	1.137	0.852	0.632
filter_on_max_peptides	0.505	0.309	0.255
filter_on_min_peptides	1.109	1.160	0.303
filter_proteotypic_peptides	0.769	0.811	0.223
import_data	0.702	0.037	0.765
load_mart	0.391	0.015	25.147
mscore4assayfdr	0.365	0.027	0.392
mscore4pepfdr	0.326	0.010	0.339
mscore4protfdr	0.304	0.008	0.313
plot.fdr_cube	0.198	0.007	0.207
plot.fdr_table	0.170	0.004	0.175
plot_correlation_between_samples	0.722	0.015	0.740
plot_variation	0.634	0.026	0.662
plot_variation_vs_total	0.655	0.029	0.722
reduce_OpenSWATH_output	0.176	0.001	0.182
removeDecoyProteins	0.165	0.003	0.167
sample_annotation	0.159	0.002	0.162
transform_MSstats_OpenSWATH	0.007	0.001	0.007
unifyProteinGroupLabels	0.150	0.002	0.150
write_matrix_peptides	0.204	0.011	0.215
write_matrix_proteins	0.161	0.002	0.163