Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the SWATH2stats package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SWATH2stats.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1877/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SWATH2stats 1.22.0 (landing page) Peter Blattmann
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: SWATH2stats |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SWATH2stats_1.22.0.tar.gz |
StartedAt: 2021-10-15 00:32:43 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:36:03 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 200.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SWATH2stats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SWATH2stats_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SWATH2stats.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.22.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘aLFQ’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed load_mart 4.992 0.111 8.539 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/SWATH2stats.Rcheck/00check.log’ for details.
SWATH2stats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SWATH2stats ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
SWATH2stats.Rcheck/tests/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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" [ FAIL 0 | WARN 73 | SKIP 0 | PASS 113 ] > > proc.time() user system elapsed 21.151 0.702 25.802
SWATH2stats.Rcheck/SWATH2stats-Ex.timings
name | user | system | elapsed | |
JPP_update | 0.167 | 0.004 | 0.172 | |
add_genesymbol | 0.011 | 0.001 | 0.012 | |
assess_decoy_rate | 0.145 | 0.003 | 0.149 | |
assess_fdr_byrun | 0.523 | 0.009 | 0.532 | |
assess_fdr_overall | 0.216 | 0.013 | 0.230 | |
convert4MSstats | 0.612 | 0.013 | 0.625 | |
convert4PECA | 0.150 | 0.003 | 0.153 | |
convert4aLFQ | 0.752 | 0.018 | 0.770 | |
convert4mapDIA | 0.550 | 0.014 | 0.565 | |
convert4pythonscript | 0.190 | 0.004 | 0.195 | |
convert_protein_ids | 0 | 0 | 0 | |
count_analytes | 0.186 | 0.006 | 0.192 | |
disaggregate | 0.345 | 0.017 | 0.362 | |
filter_all_peptides | 0.201 | 0.004 | 0.205 | |
filter_mscore | 0.233 | 0.010 | 0.243 | |
filter_mscore_condition | 0.173 | 0.008 | 0.180 | |
filter_mscore_fdr | 0.569 | 0.034 | 0.605 | |
filter_mscore_freqobs | 0.160 | 0.003 | 0.164 | |
filter_on_max_peptides | 0.157 | 0.005 | 0.162 | |
filter_on_min_peptides | 0.183 | 0.008 | 0.190 | |
filter_proteotypic_peptides | 0.151 | 0.004 | 0.155 | |
import_data | 0.615 | 0.024 | 0.638 | |
load_mart | 4.992 | 0.111 | 8.539 | |
mscore4assayfdr | 0.534 | 0.041 | 0.577 | |
mscore4pepfdr | 0.366 | 0.014 | 0.380 | |
mscore4protfdr | 0.323 | 0.005 | 0.329 | |
plot.fdr_cube | 0.206 | 0.006 | 0.214 | |
plot.fdr_table | 0.214 | 0.008 | 0.223 | |
plot_correlation_between_samples | 0.472 | 0.010 | 0.483 | |
plot_variation | 0.524 | 0.005 | 0.530 | |
plot_variation_vs_total | 0.491 | 0.005 | 0.497 | |
reduce_OpenSWATH_output | 0.169 | 0.004 | 0.174 | |
removeDecoyProteins | 0.156 | 0.003 | 0.160 | |
sample_annotation | 0.157 | 0.005 | 0.162 | |
transform_MSstats_OpenSWATH | 0.003 | 0.001 | 0.004 | |
unifyProteinGroupLabels | 0.140 | 0.008 | 0.147 | |
validate_columns | 0.001 | 0.001 | 0.002 | |
write_matrix_peptides | 0.170 | 0.002 | 0.173 | |
write_matrix_proteins | 0.154 | 0.002 | 0.156 | |