Package: SWATH2stats

Version: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2020-04-15 06:03:38 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:06:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 165.4 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
convert_protein_ids 1.241  0.043   6.737
* 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-3.10-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

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


* 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 17.698   3.745  21.990 

name	user	system	elapsed
JPP_update	0.188	0.009	0.197
add_genesymbol	0.010	0.001	0.011
assess_decoy_rate	0.163	0.003	0.168
assess_fdr_byrun	0.205	0.008	0.284
assess_fdr_overall	0.206	0.008	0.216
convert4MSstats	0.807	0.016	0.826
convert4PECA	0.194	0.006	0.204
convert4aLFQ	0.828	0.030	0.868
convert4mapDIA	0.822	0.036	0.878
convert4pythonscript	0.215	0.004	0.226
convert_protein_ids	1.241	0.043	6.737
count_analytes	0.174	0.006	0.180
disaggregate	0.531	0.018	0.557
filter_all_peptides	0.206	0.008	0.215
filter_mscore_all	0.544	0.163	0.253
filter_mscore_fdr	1.055	0.922	0.635
filter_on_max_peptides	0.419	0.290	0.258
filter_on_min_peptides	0.893	1.267	0.281
filter_proteotypic_peptides	0.675	0.883	0.232
import_data	0.594	0.030	0.635
load_mart	0.386	0.013	2.027
mscore4assayfdr	0.381	0.026	0.408
mscore4pepfdr	0.382	0.012	0.395
mscore4protfdr	0.326	0.013	0.338
plot.fdr_cube	0.193	0.002	0.196
plot.fdr_table	0.200	0.007	0.209
plot_correlation_between_samples	0.739	0.007	0.754
plot_variation	0.647	0.022	0.676
plot_variation_vs_total	0.563	0.025	0.589
reduce_OpenSWATH_output	0.173	0.002	0.177
removeDecoyProteins	0.198	0.003	0.201
sample_annotation	0.170	0.002	0.174
transform_MSstats_OpenSWATH	0.007	0.001	0.007
unifyProteinGroupLabels	0.185	0.005	0.190
write_matrix_peptides	0.207	0.008	0.218
write_matrix_proteins	0.149	0.003	0.154