Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MSstatsConvert package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsConvert.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 1209/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstatsConvert 1.2.2 (landing page) Mateusz Staniak
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MSstatsConvert |
Version: 1.2.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsConvert_1.2.2.tar.gz |
StartedAt: 2021-10-14 21:28:48 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:29:32 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 44.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSstatsConvert.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsConvert.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsConvert_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsConvert.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 ‘MSstatsConvert/DESCRIPTION’ ... OK * this is package ‘MSstatsConvert’ version ‘1.2.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘MSstatsConvert’ 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tinytest.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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/MSstatsConvert.Rcheck/00check.log’ for details.
MSstatsConvert.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstatsConvert ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘MSstatsConvert’ ... ** using staged installation ** R ** 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 (MSstatsConvert)
MSstatsConvert.Rcheck/tests/tinytest.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. > > if (requireNamespace("tinytest", quietly = TRUE)) { + MSstatsConvert::MSstatsLogsSettings(FALSE, FALSE, TRUE) + tinytest::test_package("MSstatsConvert") + } test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 0 tests test_MSstatsConvert.R......... 1 tests [0;32mOK[0m test_MSstatsConvert.R......... 2 tests [0;32mOK[0m test_MSstatsConvert.R......... 3 tests [0;32mOK[0m test_MSstatsConvert.R......... 4 tests [0;32mOK[0m test_MSstatsConvert.R......... 5 tests [0;32mOK[0m test_MSstatsConvert.R......... 6 tests [0;32mOK[0m [0;34m0.2s[0m test_annotation.R............. 0 tests test_annotation.R............. 0 tests test_annotation.R............. 0 tests test_annotation.R............. 0 tests test_annotation.R............. 0 tests test_annotation.R............. 0 tests test_annotation.R............. 0 tests test_annotation.R............. 0 tests INFO [2021-10-14 21:29:21] ** Using annotation extracted from quantification data. INFO [2021-10-14 21:29:21] ** Run labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 1 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. INFO [2021-10-14 21:29:21] ** Run labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 2 tests [0;32mOK[0m test_annotation.R............. 2 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. INFO [2021-10-14 21:29:21] ** Run labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 3 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. INFO [2021-10-14 21:29:21] ** Run labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 4 tests [0;32mOK[0m test_annotation.R............. 4 tests [0;32mOK[0m test_annotation.R............. 4 tests [0;32mOK[0m test_annotation.R............. 5 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Run annotation merged with quantification data. test_annotation.R............. 6 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. INFO [2021-10-14 21:29:21] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 6 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Run annotation merged with quantification data. test_annotation.R............. 7 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. INFO [2021-10-14 21:29:21] ** Run labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 7 tests [0;32mOK[0m test_annotation.R............. 8 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. INFO [2021-10-14 21:29:21] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. test_annotation.R............. 8 tests [0;32mOK[0m test_annotation.R............. 9 tests [0;32mOK[0m test_annotation.R............. 10 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Using provided annotation. test_annotation.R............. 11 tests [0;32mOK[0m [0;36m92ms[0m test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 0 tests test_balanced_design.R........ 1 tests [0;32mOK[0m test_balanced_design.R........ 2 tests [0;32mOK[0m test_balanced_design.R........ 3 tests [0;32mOK[0m test_balanced_design.R........ 3 tests [0;32mOK[0m test_balanced_design.R........ 3 tests [0;32mOK[0m test_balanced_design.R........ 3 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 4 tests [0;32mOK[0m test_balanced_design.R........ 5 tests [0;32mOK[0m test_balanced_design.R........ 5 tests [0;32mOK[0m test_balanced_design.R........ 6 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 7 tests [0;32mOK[0m test_balanced_design.R........ 8 tests [0;32mOK[0m test_balanced_design.R........ 9 tests [0;32mOK[0m test_balanced_design.R........ 10 tests [0;32mOK[0m test_balanced_design.R........ 11 tests [0;32mOK[0m [0;34m0.1s[0m test_cleanRaw.R............... 0 tests test_cleanRaw.R............... 0 tests test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire imported successfully. test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire imported successfully. test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire imported successfully. test_cleanRaw.R............... 0 tests test_cleanRaw.R............... 0 tests test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire imported successfully. test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Using selected fragments and peptides. INFO [2021-10-14 21:29:21] ** Extracted the data from selected fragments and/or peptides. INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire cleaned successfully. test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Using selected fragments and peptides. INFO [2021-10-14 21:29:21] ** Extracted the data from selected fragments and/or peptides. INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire cleaned successfully. test_cleanRaw.R............... 0 tests INFO [2021-10-14 21:29:21] ** Using selected fragments. INFO [2021-10-14 21:29:21] ** Extracted the data from selected fragments and/or peptides. INFO [2021-10-14 21:29:21] ** Raw data from DIAUmpire cleaned successfully. test_cleanRaw.R............... 0 tests test_cleanRaw.R............... 1 tests [0;32mOK[0m test_cleanRaw.R............... 2 tests [0;32mOK[0m test_cleanRaw.R............... 3 tests [0;32mOK[0m test_cleanRaw.R............... 4 tests [0;32mOK[0m test_cleanRaw.R............... 5 tests [0;32mOK[0m test_cleanRaw.R............... 6 tests [0;32mOK[0m test_cleanRaw.R............... 7 tests [0;32mOK[0m test_cleanRaw.R............... 8 tests [0;32mOK[0m test_cleanRaw.R............... 9 tests [0;32mOK[0m test_cleanRaw.R............... 9 tests [0;32mOK[0m test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Raw data from MaxQuant imported successfully. test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed. INFO [2021-10-14 21:29:21] ** Raw data from MaxQuant cleaned successfully. test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Onlyidentifiedbysite equal to + are removed INFO [2021-10-14 21:29:21] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed. INFO [2021-10-14 21:29:21] ** Raw data from MaxQuant cleaned successfully. test_cleanRaw.R............... 9 tests [0;32mOK[0m test_cleanRaw.R............... 10 tests [0;32mOK[0m test_cleanRaw.R............... 11 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed. INFO [2021-10-14 21:29:21] ** Raw data from MaxQuant cleaned successfully. test_cleanRaw.R............... 12 tests [0;32mOK[0m test_cleanRaw.R............... 13 tests [0;32mOK[0m test_cleanRaw.R............... 13 tests [0;32mOK[0m test_cleanRaw.R............... 13 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Raw data from MaxQuant imported successfully. test_cleanRaw.R............... 13 tests [0;32mOK[0m INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2021-10-14 21:29:21] ** Rows with values of Reverse equal to + are removed INFO [2021-10-14 21:29:21] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed. INFO [2021-10-14 21:29:22] ** Features with all missing measurements across channels within each run are removed. INFO [2021-10-14 21:29:22] ** Raw data from MaxQuant cleaned successfully. test_cleanRaw.R............... 13 tests [0;32mOK[0m test_cleanRaw.R............... 14 tests [0;32mOK[0m test_cleanRaw.R............... 15 tests [0;32mOK[0m test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenMS imported successfully. test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenMS imported successfully. test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenMS cleaned successfully. test_cleanRaw.R............... 15 tests [0;32mOK[0m test_cleanRaw.R............... 16 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenMS cleaned successfully. test_cleanRaw.R............... 17 tests [0;32mOK[0m test_cleanRaw.R............... 18 tests [0;32mOK[0m test_cleanRaw.R............... 18 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenMS imported successfully. test_cleanRaw.R............... 18 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenMS cleaned successfully. test_cleanRaw.R............... 18 tests [0;32mOK[0m test_cleanRaw.R............... 19 tests [0;32mOK[0m test_cleanRaw.R............... 20 tests [0;32mOK[0m test_cleanRaw.R............... 20 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenSWATH imported successfully. test_cleanRaw.R............... 20 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from OpenSWATH cleaned successfully. test_cleanRaw.R............... 20 tests [0;32mOK[0m test_cleanRaw.R............... 21 tests [0;32mOK[0m test_cleanRaw.R............... 22 tests [0;32mOK[0m test_cleanRaw.R............... 22 tests [0;32mOK[0m test_cleanRaw.R............... 22 tests [0;32mOK[0m test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer imported successfully. test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer imported successfully. test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer cleaned successfully. test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer cleaned successfully. test_cleanRaw.R............... 22 tests [0;32mOK[0m test_cleanRaw.R............... 23 tests [0;32mOK[0m test_cleanRaw.R............... 24 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer imported successfully. test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer imported successfully. test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer imported successfully. test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer cleaned successfully. test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer cleaned successfully. test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from ProteomeDiscoverer cleaned successfully. test_cleanRaw.R............... 25 tests [0;32mOK[0m test_cleanRaw.R............... 26 tests [0;32mOK[0m test_cleanRaw.R............... 27 tests [0;32mOK[0m test_cleanRaw.R............... 28 tests [0;32mOK[0m test_cleanRaw.R............... 29 tests [0;32mOK[0m test_cleanRaw.R............... 30 tests [0;32mOK[0m test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Progenesis imported successfully. test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Progenesis imported successfully. test_cleanRaw.R............... 30 tests [0;32mOK[0m test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Progenesis cleaned successfully. test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Progenesis cleaned successfully. test_cleanRaw.R............... 30 tests [0;32mOK[0m test_cleanRaw.R............... 31 tests [0;32mOK[0m test_cleanRaw.R............... 32 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Skyline imported successfully. test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Skyline imported successfully. test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Skyline imported successfully. test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Skyline cleaned successfully. test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Skyline cleaned successfully. test_cleanRaw.R............... 33 tests [0;32mOK[0m test_cleanRaw.R............... 34 tests [0;32mOK[0m test_cleanRaw.R............... 35 tests [0;32mOK[0m test_cleanRaw.R............... 36 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Skyline cleaned successfully. test_cleanRaw.R............... 37 tests [0;32mOK[0m test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from SpectroMine imported successfully. test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from SpectroMine imported successfully. test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from SpectroMine cleaned successfully. test_cleanRaw.R............... 37 tests [0;32mOK[0m test_cleanRaw.R............... 38 tests [0;32mOK[0m test_cleanRaw.R............... 39 tests [0;32mOK[0m ERROR [2021-10-14 21:29:22] There is no channel intensity column in the input data, which should start with 'PSM' and end with 'Raw'. test_cleanRaw.R............... 40 tests [0;32mOK[0m test_cleanRaw.R............... 40 tests [0;32mOK[0m test_cleanRaw.R............... 40 tests [0;32mOK[0m test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Spectronaut imported successfully. test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Spectronaut imported successfully. test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Spectronaut cleaned successfully. test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Raw data from Spectronaut cleaned successfully. test_cleanRaw.R............... 40 tests [0;32mOK[0m test_cleanRaw.R............... 41 tests [0;32mOK[0m test_cleanRaw.R............... 42 tests [0;32mOK[0m test_cleanRaw.R............... 43 tests [0;32mOK[0m [0;34m1.1s[0m test_dt.R..................... 0 tests test_dt.R..................... 0 tests test_dt.R..................... 1 tests [0;32mOK[0m test_dt.R..................... 2 tests [0;32mOK[0m test_dt.R..................... 3 tests [0;32mOK[0m test_dt.R..................... 4 tests [0;32mOK[0m test_dt.R..................... 5 tests [0;32mOK[0m test_dt.R..................... 6 tests [0;32mOK[0m test_dt.R..................... 6 tests [0;32mOK[0m test_dt.R..................... 7 tests [0;32mOK[0m test_dt.R..................... 7 tests [0;32mOK[0m test_dt.R..................... 7 tests [0;32mOK[0m test_dt.R..................... 8 tests [0;32mOK[0m test_dt.R..................... 9 tests [0;32mOK[0m test_dt.R..................... 10 tests [0;32mOK[0m [0;36m15ms[0m test_feature_cleaning.R....... 0 tests test_feature_cleaning.R....... 0 tests test_feature_cleaning.R....... 0 tests test_feature_cleaning.R....... 0 tests INFO [2021-10-14 21:29:22] ** Features with one or two measurements across channels within each run are removed. test_feature_cleaning.R....... 1 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Features with one or two measurements across runs are removed. test_feature_cleaning.R....... 2 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Features with one or two measurements across runs are removed. test_feature_cleaning.R....... 3 tests [0;32mOK[0m test_feature_cleaning.R....... 3 tests [0;32mOK[0m test_feature_cleaning.R....... 3 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Features with all missing measurements across runs are removed. test_feature_cleaning.R....... 4 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Features with one or two measurements across runs are removed. test_feature_cleaning.R....... 5 tests [0;32mOK[0m test_feature_cleaning.R....... 5 tests [0;32mOK[0m test_feature_cleaning.R....... 5 tests [0;32mOK[0m test_feature_cleaning.R....... 6 tests [0;32mOK[0m test_feature_cleaning.R....... 6 tests [0;32mOK[0m test_feature_cleaning.R....... 6 tests [0;32mOK[0m test_feature_cleaning.R....... 6 tests [0;32mOK[0m test_feature_cleaning.R....... 7 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Three isotopic preaks per feature and run are summed test_feature_cleaning.R....... 8 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 9 tests [0;32mOK[0m test_feature_cleaning.R....... 10 tests [0;32mOK[0m test_feature_cleaning.R....... 10 tests [0;32mOK[0m test_feature_cleaning.R....... 10 tests [0;32mOK[0m test_feature_cleaning.R....... 11 tests [0;32mOK[0m test_feature_cleaning.R....... 11 tests [0;32mOK[0m test_feature_cleaning.R....... 11 tests [0;32mOK[0m test_feature_cleaning.R....... 12 tests [0;32mOK[0m test_feature_cleaning.R....... 12 tests [0;32mOK[0m test_feature_cleaning.R....... 13 tests [0;32mOK[0m test_feature_cleaning.R....... 13 tests [0;32mOK[0m test_feature_cleaning.R....... 14 tests [0;32mOK[0m test_feature_cleaning.R....... 14 tests [0;32mOK[0m test_feature_cleaning.R....... 14 tests [0;32mOK[0m test_feature_cleaning.R....... 14 tests [0;32mOK[0m test_feature_cleaning.R....... 14 tests [0;32mOK[0m test_feature_cleaning.R....... 14 tests [0;32mOK[0m test_feature_cleaning.R....... 15 tests [0;32mOK[0m test_feature_cleaning.R....... 15 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** PSMs have been aggregated to peptide ions. test_feature_cleaning.R....... 16 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** PSMs have been aggregated to peptide ions. test_feature_cleaning.R....... 16 tests [0;32mOK[0m test_feature_cleaning.R....... 17 tests [0;32mOK[0m test_feature_cleaning.R....... 17 tests [0;32mOK[0m test_feature_cleaning.R....... 17 tests [0;32mOK[0m test_feature_cleaning.R....... 18 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] Proteins with a single feature are removed. test_feature_cleaning.R....... 19 tests [0;32mOK[0m test_feature_cleaning.R....... 20 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2021-10-14 21:29:22] ** Features with one or two measurements across runs are removed. test_feature_cleaning.R....... 20 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Features with one or two measurements across channels within each run are removed. INFO [2021-10-14 21:29:22] ** PSMs have been aggregated to peptide ions. test_feature_cleaning.R....... 20 tests [0;32mOK[0m test_feature_cleaning.R....... 21 tests [0;32mOK[0m test_feature_cleaning.R....... 22 tests [0;32mOK[0m [0;34m0.4s[0m test_filtering.R.............. 0 tests test_filtering.R.............. 0 tests test_filtering.R.............. 1 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Sequences containing \+ are removed. test_filtering.R.............. 2 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Sequences containing \+ are removed. test_filtering.R.............. 3 tests [0;32mOK[0m test_filtering.R.............. 4 tests [0;32mOK[0m test_filtering.R.............. 5 tests [0;32mOK[0m test_filtering.R.............. 6 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to - are removed test_filtering.R.............. 7 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to +, - are removed test_filtering.R.............. 8 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to + are removed test_filtering.R.............. 9 tests [0;32mOK[0m test_filtering.R.............. 10 tests [0;32mOK[0m test_filtering.R.............. 11 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to R are removed test_filtering.R.............. 12 tests [0;32mOK[0m test_filtering.R.............. 13 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to + are removed INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_2 equal to + are removed test_filtering.R.............. 14 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to X are removed INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_2 equal to X are removed test_filtering.R.............. 15 tests [0;32mOK[0m test_filtering.R.............. 16 tests [0;32mOK[0m test_filtering.R.............. 17 tests [0;32mOK[0m test_filtering.R.............. 18 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values greater than 0.3 in Score are removed test_filtering.R.............. 19 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values greater than 0.3 in Score are removed test_filtering.R.............. 20 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values greater than 0.3 in Score are removed test_filtering.R.............. 21 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values greater than 0.3 in Score are removed test_filtering.R.............. 22 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values smaller than 0.3 in Score are removed test_filtering.R.............. 23 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values smaller than 0.3 in Score are removed test_filtering.R.............. 24 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values smaller than 0.3 in Score are removed test_filtering.R.............. 25 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values smaller than 0.3 in Score are removed test_filtering.R.............. 26 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Intensities with values greater than 0.3 in Score are replaced with NA test_filtering.R.............. 26 tests [0;32mOK[0m test_filtering.R.............. 27 tests [0;32mOK[0m test_filtering.R.............. 28 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Intensities with values greater than 0.3 in Score are replaced with NA test_filtering.R.............. 28 tests [0;32mOK[0m test_filtering.R.............. 29 tests [0;32mOK[0m test_filtering.R.............. 30 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Intensities with values smaller than 0.3 in Score are replaced with NA test_filtering.R.............. 30 tests [0;32mOK[0m test_filtering.R.............. 31 tests [0;32mOK[0m test_filtering.R.............. 32 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Intensities with values smaller than 0.3 in Score are replaced with NA test_filtering.R.............. 32 tests [0;32mOK[0m test_filtering.R.............. 33 tests [0;32mOK[0m test_filtering.R.............. 34 tests [0;32mOK[0m test_filtering.R.............. 35 tests [0;32mOK[0m INFO [2021-10-14 21:29:22] ** Rows with values of Symbol_1 equal to + are removed INFO [2021-10-14 21:29:22] ** Sequences containing \+ are removed. test_filtering.R.............. 36 tests [0;32mOK[0m INFO [2021-10-14 21:29:23] ** Rows with values of Symbol_1 equal to + are removed INFO [2021-10-14 21:29:23] ** Sequences containing \+ are removed. test_filtering.R.............. 37 tests [0;32mOK[0m [0;36m60ms[0m test_fractions.R.............. 0 tests test_fractions.R.............. 1 tests [0;32mOK[0m test_fractions.R.............. 1 tests [0;32mOK[0m test_fractions.R.............. 1 tests [0;32mOK[0m test_fractions.R.............. 1 tests [0;32mOK[0m test_fractions.R.............. 1 tests [0;32mOK[0m test_fractions.R.............. 1 tests [0;32mOK[0m test_fractions.R.............. 2 tests [0;32mOK[0m test_fractions.R.............. 3 tests [0;32mOK[0m test_fractions.R.............. 4 tests [0;32mOK[0m test_fractions.R.............. 4 tests [0;32mOK[0m test_fractions.R.............. 5 tests [0;32mOK[0m test_fractions.R.............. 5 tests [0;32mOK[0m test_fractions.R.............. 5 tests [0;32mOK[0m test_fractions.R.............. 5 tests [0;32mOK[0m test_fractions.R.............. 6 tests [0;32mOK[0m test_fractions.R.............. 7 tests [0;32mOK[0m test_fractions.R.............. 8 tests [0;32mOK[0m test_fractions.R.............. 8 tests [0;32mOK[0m INFO [2021-10-14 21:29:23] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance. INFO [2021-10-14 21:29:23] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance. INFO [2021-10-14 21:29:23] ** For peptides overlapped between fractions of 2_1 use the fraction with maximal average abundance. test_fractions.R.............. 8 tests [0;32mOK[0m test_fractions.R.............. 9 tests [0;32mOK[0m [0;34m0.1s[0m test_logging.R................ 1 tests [0;32mOK[0m test_logging.R................ 2 tests [0;32mOK[0m test_logging.R................ 3 tests [0;32mOK[0m [0;36m4ms[0m test_shared_peptides.R........ 0 tests test_shared_peptides.R........ 0 tests INFO [2021-10-14 21:29:23] ** Shared peptides are removed. test_shared_peptides.R........ 0 tests test_shared_peptides.R........ 0 tests INFO [2021-10-14 21:29:23] ** Shared peptides are removed. test_shared_peptides.R........ 0 tests test_shared_peptides.R........ 1 tests [0;32mOK[0m test_shared_peptides.R........ 2 tests [0;32mOK[0m test_shared_peptides.R........ 3 tests [0;32mOK[0m test_shared_peptides.R........ 4 tests [0;32mOK[0m test_shared_peptides.R........ 5 tests [0;32mOK[0m [0;36m20ms[0m test_workflow.R............... 0 tests test_workflow.R............... 0 tests INFO [2021-10-14 21:29:23] ** Raw data from OpenMS imported successfully. test_workflow.R............... 0 tests test_workflow.R............... 1 tests [0;32mOK[0m INFO [2021-10-14 21:29:23] ** Raw data from OpenMS cleaned successfully. test_workflow.R............... 1 tests [0;32mOK[0m test_workflow.R............... 2 tests [0;32mOK[0m INFO [2021-10-14 21:29:23] ** Using annotation extracted from quantification data. INFO [2021-10-14 21:29:23] ** Run labels were standardized to remove symbols such as '.' or '%'. test_workflow.R............... 2 tests [0;32mOK[0m test_workflow.R............... 3 tests [0;32mOK[0m INFO [2021-10-14 21:29:23] ** The following options are used: - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge - Shared peptides will be removed. - Proteins with a single feature will be removed. - Features with less than 3 measurements across runs will be removed. INFO [2021-10-14 21:29:23] ** Features with all missing measurements across runs are removed. INFO [2021-10-14 21:29:23] ** Shared peptides are removed. INFO [2021-10-14 21:29:23] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2021-10-14 21:29:23] ** Features with one or two measurements across runs are removed. INFO [2021-10-14 21:29:23] Proteins with a single feature are removed. INFO [2021-10-14 21:29:23] ** Run annotation merged with quantification data. test_workflow.R............... 3 tests [0;32mOK[0m test_workflow.R............... 4 tests [0;32mOK[0m test_workflow.R............... 5 tests [0;32mOK[0m test_workflow.R............... 6 tests [0;32mOK[0m INFO [2021-10-14 21:29:23] ** Features with one or two measurements across runs are removed. INFO [2021-10-14 21:29:23] ** Fractionation handled. INFO [2021-10-14 21:29:23] ** Updated quantification data to make balanced design. Missing values are marked by NA test_workflow.R............... 6 tests [0;32mOK[0m test_workflow.R............... 7 tests [0;32mOK[0m test_workflow.R............... 8 tests [0;32mOK[0m [0;36m80ms[0m All ok, 165 results (2.2s) There were 29 warnings (use warnings() to see them) > > > proc.time() user system elapsed 2.702 0.201 2.910
MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings
name | user | system | elapsed | |
MSstatsBalancedDesign | 0.069 | 0.006 | 0.075 | |
MSstatsClean | 0.246 | 0.017 | 0.265 | |
MSstatsImport | 0.116 | 0.007 | 0.122 | |
MSstatsLogsSettings | 0.076 | 0.002 | 0.080 | |
MSstatsMakeAnnotation | 0.251 | 0.007 | 0.259 | |
MSstatsPreprocess | 0.219 | 0.011 | 0.231 | |
MSstatsSaveSessionInfo | 0.014 | 0.006 | 0.020 | |
getDataType | 0.107 | 0.005 | 0.112 | |
getInputFile | 0.160 | 0.012 | 0.173 | |