Multiple platform build/check report for BioC 3.8 - CHECK report for SWATH2stats on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SWATH2stats_1.12.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.1’
* 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 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 6.640  0.020   1.370
filter_on_max_peptides 6.464  0.016   1.332
convert_protein_ids    0.564  0.012   5.034
* 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-3.8-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL SWATH2stats
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 
 27.280   0.228  29.713

Example timings

name	user	system	elapsed
add_genesymbol	0.016	0.000	0.039
assess_decoy_rate	0.172	0.008	0.689
assess_fdr_byrun	0.248	0.008	0.478
assess_fdr_overall	0.148	0.000	0.149
convert4MSstats	0.680	0.016	0.705
convert4PECA	0.224	0.000	0.224
convert4aLFQ	0.892	0.008	0.903
convert4mapDIA	0.808	0.012	0.834
convert4pythonscript	0.208	0.004	0.214
convert_protein_ids	0.564	0.012	5.034
count_analytes	0.200	0.000	0.202
disaggregate	0.416	0.012	0.427
filter_all_peptides	0.136	0.000	0.135
filter_mscore_all	0.788	0.008	0.300
filter_mscore_fdr	0.604	0.000	0.603
filter_on_max_peptides	6.464	0.016	1.332
filter_on_min_peptides	6.64	0.02	1.37
filter_proteotypic_peptides	0.216	0.004	0.219
import_data	0.720	0.012	0.735
load_mart	0.448	0.012	4.432
mscore4assayfdr	0.408	0.004	0.414
mscore4pepfdr	0.456	0.000	0.458
mscore4protfdr	0.276	0.004	0.280
plot.fdr_cube	0.184	0.000	0.185
plot.fdr_table	0.148	0.000	0.145
plot_correlation_between_samples	0.700	0.004	0.704
plot_variation	0.560	0.012	0.574
plot_variation_vs_total	0.528	0.008	0.537
reduce_OpenSWATH_output	0.168	0.000	0.168
removeDecoyProteins	0.164	0.000	0.163
sample_annotation	0.116	0.000	0.115
transform_MSstats_OpenSWATH	0.004	0.000	0.014
unifyProteinGroupLabels	0.124	0.000	0.122
write_matrix_peptides	0.188	0.000	0.189
write_matrix_proteins	0.192	0.004	0.199

CHECK report for SWATH2stats on malbec1

Summary

Command output

Installation output

Tests output

Example timings