Package: SWATH2stats

Version: 1.8.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SWATH2stats_1.8.1.tar.gz

StartedAt: 2018-04-12 03:14:43 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:15:38 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 55.4 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SWATH2stats_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.1’
* 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 loading without being on the library search path ... 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 installed files from ‘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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

* installing *source* package ‘SWATH2stats’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SWATH2stats)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 10.864   0.068  10.696 

name	user	system	elapsed
assess_decoy_rate	0.280	0.008	0.289
assess_fdr_byrun	0.328	0.004	0.328
assess_fdr_overall	0.304	0.000	0.304
convert4MSstats	0.868	0.008	0.878
convert4PECA	0.400	0.000	0.401
convert4aLFQ	0.604	0.004	0.608
convert4mapDIA	0.732	0.004	0.734
convert4pythonscript	0.224	0.000	0.223
count_analytes	0.220	0.004	0.222
disaggregate	0.472	0.004	0.476
filter_all_peptides	0.280	0.000	0.283
filter_mscore_all	0.272	0.000	0.261
filter_mscore_fdr	0.464	0.000	0.466
filter_on_max_peptides	0.400	0.004	0.294
filter_on_min_peptides	0.416	0.004	0.314
filter_proteotypic_peptides	0.248	0.000	0.250
import_data	0.504	0.008	0.514
mscore4assayfdr	0.484	0.000	0.481
mscore4pepfdr	0.380	0.000	0.379
mscore4protfdr	0.308	0.004	0.312
plot.fdr_cube	0.344	0.000	0.343
plot.fdr_table	0.348	0.000	0.350
plot_correlation_between_samples	1.132	0.004	1.140
plot_variation	1.316	0.012	1.329
plot_variation_vs_total	0.628	0.008	0.638
reduce_OpenSWATH_output	0.228	0.004	0.233
removeDecoyProteins	0.224	0.000	0.224
sample_annotation	0.228	0.000	0.230
transform_MSstats_OpenSWATH	0.008	0.000	0.005
unifyProteinGroupLabels	0.224	0.004	0.230
write_matrix_peptides	0.236	0.008	0.245
write_matrix_proteins	0.224	0.000	0.224