Peter Blattmann
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/SWATH2stats |
| Branch: RELEASE_3_7 |
| Last Commit: 0a5ebec |
| Last Changed Date: 2018-06-15 11:08:09 -0400 (Fri, 15 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:28:09 -0400 (Wed, 17 Oct 2018).
| Package 1453/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SWATH2stats 1.10.2 Peter Blattmann
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SWATH2stats |
| Version: 1.10.2 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SWATH2stats_1.10.2.tar.gz |
| StartedAt: 2018-10-16 04:05:16 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 04:05:59 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 42.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SWATH2stats.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SWATH2stats_1.10.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/SWATH2stats.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.10.2’ * 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 * 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-3.7-bioc/meat/SWATH2stats.Rcheck/00check.log’ for details.
SWATH2stats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL SWATH2stats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-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)
SWATH2stats.Rcheck/tests/test-all.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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
7.120 0.084 6.952
SWATH2stats.Rcheck/SWATH2stats-Ex.timings
| name | user | system | elapsed | |
| assess_decoy_rate | 0.176 | 0.012 | 0.209 | |
| assess_fdr_byrun | 0.220 | 0.004 | 0.238 | |
| assess_fdr_overall | 0.212 | 0.016 | 0.227 | |
| convert4MSstats | 0.356 | 0.012 | 0.368 | |
| convert4PECA | 0.156 | 0.000 | 0.156 | |
| convert4aLFQ | 0.376 | 0.000 | 0.377 | |
| convert4mapDIA | 0.456 | 0.016 | 0.474 | |
| convert4pythonscript | 0.124 | 0.000 | 0.125 | |
| count_analytes | 0.12 | 0.00 | 0.12 | |
| disaggregate | 0.392 | 0.004 | 0.396 | |
| filter_all_peptides | 0.120 | 0.000 | 0.119 | |
| filter_mscore_all | 0.172 | 0.004 | 0.164 | |
| filter_mscore_fdr | 0.340 | 0.004 | 0.345 | |
| filter_on_max_peptides | 0.288 | 0.008 | 0.190 | |
| filter_on_min_peptides | 0.276 | 0.004 | 0.184 | |
| filter_proteotypic_peptides | 0.168 | 0.000 | 0.166 | |
| import_data | 0.476 | 0.008 | 0.500 | |
| mscore4assayfdr | 0.268 | 0.004 | 0.274 | |
| mscore4pepfdr | 0.252 | 0.000 | 0.253 | |
| mscore4protfdr | 0.224 | 0.000 | 0.224 | |
| plot.fdr_cube | 0.144 | 0.000 | 0.144 | |
| plot.fdr_table | 0.152 | 0.000 | 0.150 | |
| plot_correlation_between_samples | 0.544 | 0.000 | 0.544 | |
| plot_variation | 0.472 | 0.008 | 0.481 | |
| plot_variation_vs_total | 0.568 | 0.008 | 0.578 | |
| reduce_OpenSWATH_output | 0.120 | 0.000 | 0.117 | |
| removeDecoyProteins | 0.128 | 0.000 | 0.130 | |
| sample_annotation | 0.112 | 0.000 | 0.114 | |
| transform_MSstats_OpenSWATH | 0.008 | 0.000 | 0.017 | |
| unifyProteinGroupLabels | 0.120 | 0.000 | 0.122 | |
| write_matrix_peptides | 0.136 | 0.000 | 0.134 | |
| write_matrix_proteins | 0.12 | 0.00 | 0.12 | |