Package: SWATH2stats

Version: 1.14.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SWATH2stats_1.14.0.tar.gz

StartedAt: 2019-10-16 05:20:59 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:23:39 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 160.0 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SWATH2stats_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
filter_on_min_peptides 5.912  0.017   1.059
convert_protein_ids    0.462  0.008  13.353
* 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-3.9-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SWATH2stats
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-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: 113 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 19.373   0.255  37.149 

name	user	system	elapsed
JPP_update	0.184	0.000	0.185
add_genesymbol	0.014	0.000	0.014
assess_decoy_rate	0.165	0.008	0.174
assess_fdr_byrun	0.248	0.000	0.248
assess_fdr_overall	0.162	0.000	0.162
convert4MSstats	0.68	0.02	0.70
convert4PECA	0.179	0.000	0.179
convert4aLFQ	0.570	0.003	0.574
convert4mapDIA	0.504	0.012	0.516
convert4pythonscript	0.124	0.004	0.129
convert_protein_ids	0.462	0.008	13.353
count_analytes	0.204	0.000	0.204
disaggregate	0.540	0.008	0.549
filter_all_peptides	0.486	0.000	0.485
filter_mscore_all	0.928	0.000	0.348
filter_mscore_fdr	0.538	0.000	0.538
filter_on_max_peptides	2.893	0.007	0.556
filter_on_min_peptides	5.912	0.017	1.059
filter_proteotypic_peptides	0.197	0.000	0.197
import_data	0.709	0.012	0.724
load_mart	0.398	0.004	2.561
mscore4assayfdr	0.461	0.012	0.474
mscore4pepfdr	0.268	0.000	0.267
mscore4protfdr	0.267	0.000	0.269
plot.fdr_cube	0.137	0.000	0.138
plot.fdr_table	0.149	0.008	0.157
plot_correlation_between_samples	0.499	0.004	0.503
plot_variation	0.432	0.012	0.444
plot_variation_vs_total	0.591	0.008	0.600
reduce_OpenSWATH_output	0.189	0.000	0.189
removeDecoyProteins	0.202	0.000	0.201
sample_annotation	0.176	0.004	0.180
transform_MSstats_OpenSWATH	0.003	0.004	0.006
unifyProteinGroupLabels	0.182	0.004	0.187
write_matrix_peptides	0.228	0.004	0.233
write_matrix_proteins	0.199	0.000	0.198