Package: SWATH2stats

Version: 1.13.5

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_1.13.5.tar.gz

StartedAt: 2019-04-09 03:57:15 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:00:28 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 192.7 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.13.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.13.5’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
filter_on_max_peptides 5.944  0.068   1.205
filter_on_min_peptides 5.698  0.036   1.196
convert_protein_ids    0.489  0.008  19.504
load_mart              0.361  0.008  18.027
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SWATH2stats
###
##############################################################################
##############################################################################


* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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: 120 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 26.668   0.293  45.326 

name	user	system	elapsed
JPP_update	0.107	0.000	0.107
add_genesymbol	0.008	0.000	0.008
assess_decoy_rate	0.116	0.000	0.117
assess_fdr_byrun	0.243	0.008	0.251
assess_fdr_overall	0.233	0.004	0.237
convert4MSstats	0.587	0.004	0.591
convert4PECA	0.144	0.000	0.145
convert4aLFQ	0.567	0.008	0.576
convert4mapDIA	0.380	0.004	0.384
convert4pythonscript	0.125	0.000	0.125
convert_protein_ids	0.489	0.008	19.504
count_analytes	0.166	0.012	0.178
disaggregate	0.315	0.012	0.327
filter_all_peptides	0.144	0.000	0.144
filter_mscore_all	0.755	0.000	0.265
filter_mscore_fdr	0.59	0.00	0.59
filter_on_max_peptides	5.944	0.068	1.205
filter_on_min_peptides	5.698	0.036	1.196
filter_proteotypic_peptides	0.188	0.008	0.197
import_data	0.522	0.012	0.534
load_mart	0.361	0.008	18.027
mscore4assayfdr	0.316	0.004	0.320
mscore4pepfdr	0.331	0.000	0.361
mscore4protfdr	0.351	0.000	0.351
plot.fdr_cube	0.275	0.004	0.279
plot.fdr_table	0.228	0.004	0.231
plot_correlation_between_samples	0.726	0.000	0.731
plot_variation	0.682	0.012	0.694
plot_variation_vs_total	0.576	0.016	0.592
reduce_OpenSWATH_output	0.198	0.008	0.205
removeDecoyProteins	0.130	0.000	0.131
sample_annotation	0.189	0.000	0.190
transform_MSstats_OpenSWATH	0.006	0.000	0.006
unifyProteinGroupLabels	0.145	0.004	0.149
write_matrix_peptides	0.223	0.004	0.227
write_matrix_proteins	0.202	0.007	0.210