| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:57 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1228/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsConvert 1.4.1 (landing page) Mateusz Staniak
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MSstatsConvert |
| Version: 1.4.1 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsConvert.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSstatsConvert_1.4.1.tar.gz |
| StartedAt: 2022-04-12 23:21:34 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:22:28 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 54.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstatsConvert.Rcheck |
| Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MSstatsConvert.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MSstatsConvert_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSstatsConvert.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MSstatsConvert/DESCRIPTION' ... OK * this is package 'MSstatsConvert' version '1.4.1' * 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 ... OK * checking for portable file names ... 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.findAvailable' '.standardizeColnames' * checking S3 generic/method consistency ... WARNING as.data.frame: function(x, row.names, optional, ...) as.data.frame.MSstatsValidated: function(x) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .cleanRawPhilosopher: no visible binding for global variable 'ModifiedPeptideSequence' .cleanRawPhilosopher: no visible binding for global variable 'PeptideSequence' .cleanRawPhilosopher: no visible binding for global variable 'IsUnique' .cleanRawPhilosopher: no visible binding for global variable 'PSM' .cleanRawPhilosopher: no visible binding for global variable 'PrecursorCharge' .cleanRawPhilosopher: no visible binding for global variable 'Intensity' .cleanRawPhilosopher: no visible binding for global variable 'Run' .cleanRawPhilosopher: no visible binding for global variable 'ProteinName' .summarizeMultiplePSMs: no visible binding for global variable 'Purity' .summarizeMultiplePSMs: no visible binding for global variable 'PeptideProphet.Probability' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'ModifiedPeptideSequence' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'PeptideSequence' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'IsUnique' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'PSM' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'PrecursorCharge' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'Intensity' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'Run' MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global variable 'ProteinName' Undefined global functions or variables: Intensity IsUnique ModifiedPeptideSequence PSM PeptideProphet.Probability PeptideSequence PrecursorCharge ProteinName Purity Run * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'getInputFile' and siglist 'MSstatsPhilosopherFiles' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'MSstatsClean' 'channels' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'tinytest.R' OK ** running tests for arch 'x64' ... 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: 3 WARNINGs, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MSstatsConvert.Rcheck/00check.log' for details.
MSstatsConvert.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MSstatsConvert_1.4.1.tar.gz && rm -rf MSstatsConvert.buildbin-libdir && mkdir MSstatsConvert.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MSstatsConvert.buildbin-libdir MSstatsConvert_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MSstatsConvert_1.4.1.zip && rm MSstatsConvert_1.4.1.tar.gz MSstatsConvert_1.4.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 583k 100 583k 0 0 1550k 0 --:--:-- --:--:-- --:--:-- 1556k
install for i386
* installing *source* package 'MSstatsConvert' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MSstatsConvert'
finding HTML links ... done
MSstatsBalancedDesign html
MSstatsClean html
MSstatsConvert html
MSstatsImport html
MSstatsInputFiles html
MSstatsLogsSettings html
MSstatsMakeAnnotation html
MSstatsPreprocess html
MSstatsSaveSessionInfo html
as.data.frame.MSstatsValidated html
as.data.table.MSstatsValidated html
dot-MSstatsFormat html
dot-addFractions html
dot-adjustIntensities html
dot-aggregatePSMstoPeptideIons html
dot-checkAnnotation html
dot-checkDDA html
dot-checkDuplicatedMeasurements html
dot-checkMSstatsParams html
dot-checkMultiRun html
dot-checkOverlappedFeatures html
dot-cleanByFeature html
dot-cleanRawDIAUmpire html
dot-cleanRawMaxQuant html
dot-cleanRawOpenMS html
dot-cleanRawOpenSWATH html
dot-cleanRawPD html
dot-cleanRawPDMSstats html
dot-cleanRawPDTMT html
dot-cleanRawPhilosopher html
dot-cleanRawProgenesis html
dot-cleanRawSkyline html
dot-cleanRawSpectroMineTMT html
dot-cleanRawSpectronaut html
dot-countCommonFeatures html
dot-fillValues html
dot-filterByPattern html
dot-filterByScore html
dot-filterExact html
dot-filterFewMeasurements html
dot-filterManyColumns html
dot-filterOverlapped html
dot-findAvailable html
dot-fixBasicColumns html
dot-fixColumnTypes html
dot-fixMissingValues html
dot-getChannelColumns html
dot-getCorrectFraction html
dot-getDataTable html
dot-getFullDesign html
dot-getMissingRunsPerFeature html
dot-getOverlappingFeatures html
dot-handleFiltering html
dot-handleFractions html
dot-handleFractionsLF html
dot-handleFractionsTMT html
dot-handleIsotopicPeaks html
dot-handleSharedPeptides html
dot-handleSingleFeaturePerProtein html
dot-logConverterOptions html
dot-logSuccess html
dot-makeBalancedDesign html
dot-makeExactFilterMessage html
dot-makeScoreFilterMessage html
dot-mergeAnnotation html
dot-nullAppender html
dot-onLoad html
dot-removeOverlappingFeatures html
dot-removeSharedPeptides html
dot-selectMSstatsColumns html
dot-standardizeColnames html
dot-summarizeMultipleMeasurements html
dot-summarizeMultiplePSMs html
getDataType html
getInputFile html
** 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
install for x64
* installing *source* package 'MSstatsConvert' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MSstatsConvert' as MSstatsConvert_1.4.1.zip
* DONE (MSstatsConvert)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MSstatsConvert' successfully unpacked and MD5 sums checked
|
MSstatsConvert.Rcheck/tests_i386/tinytest.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 [2022-04-12 23:22:13] ** Using annotation extracted from quantification data.
INFO [2022-04-12 23:22:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:13] ** Using provided annotation.
INFO [2022-04-12 23:22:13] ** 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 [2022-04-12 23:22:13] ** Using provided annotation.
INFO [2022-04-12 23:22:13] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 3 tests [0;32mOK[0m INFO [2022-04-12 23:22:13] ** Using provided annotation.
INFO [2022-04-12 23:22:13] ** 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 [2022-04-12 23:22:13] ** Run annotation merged with quantification data.
test_annotation.R............. 6 tests [0;32mOK[0m INFO [2022-04-12 23:22:13] ** Using provided annotation.
INFO [2022-04-12 23:22:13] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 6 tests [0;32mOK[0m INFO [2022-04-12 23:22:13] ** Run annotation merged with quantification data.
test_annotation.R............. 7 tests [0;32mOK[0m INFO [2022-04-12 23:22:13] ** Using provided annotation.
INFO [2022-04-12 23:22:13] ** 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 [2022-04-12 23:22:13] ** Using provided annotation.
INFO [2022-04-12 23:22:13] ** 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 [2022-04-12 23:22:13] ** Using provided annotation.
test_annotation.R............. 11 tests [0;32mOK[0m [0;34m0.2s[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;34m0.2s[0m
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Using selected fragments and peptides.
INFO [2022-04-12 23:22:14] ** Extracted the data from selected fragments and/or peptides.
INFO [2022-04-12 23:22:14] ** Raw data from DIAUmpire cleaned successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Using selected fragments and peptides.
INFO [2022-04-12 23:22:14] ** Extracted the data from selected fragments and/or peptides.
INFO [2022-04-12 23:22:14] ** Raw data from DIAUmpire cleaned successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:14] ** Using selected fragments.
INFO [2022-04-12 23:22:14] ** Extracted the data from selected fragments and/or peptides.
INFO [2022-04-12 23:22:14] ** 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 [2022-04-12 23:22:15] ** Raw data from MaxQuant imported successfully.
test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-04-12 23:22:15] ** Raw data from MaxQuant cleaned successfully.
test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Onlyidentifiedbysite equal to + are removed
INFO [2022-04-12 23:22:15] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from MaxQuant imported successfully.
test_cleanRaw.R............... 13 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:15] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:15] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-04-12 23:22:15] ** Features with all missing measurements across channels within each run are removed.
INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from OpenMS cleaned successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m
test_cleanRaw.R............... 16 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 18 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from OpenSWATH imported successfully.
test_cleanRaw.R............... 20 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** 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 [2022-04-12 23:22:15] ** Raw data from Progenesis imported successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2022-04-12 23:22:15] ** Raw data from Progenesis imported successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from Progenesis cleaned successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** 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 [2022-04-12 23:22:16] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from Skyline cleaned successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** 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 [2022-04-12 23:22:16] ** Raw data from Skyline cleaned successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from SpectroMine imported successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from SpectroMine imported successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** 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 [2022-04-12 23:22:16] 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 [2022-04-12 23:22:16] ** Raw data from Spectronaut imported successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from Spectronaut imported successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Raw data from Spectronaut cleaned successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** 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;34m2.5s[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;36m16ms[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 [2022-04-12 23:22:16] ** Features with one or two measurements across channels within each run are removed.
test_feature_cleaning.R....... 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** Features with one or two measurements across runs are removed.
test_feature_cleaning.R....... 2 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** 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 [2022-04-12 23:22:16] ** Features with all missing measurements across runs are removed.
test_feature_cleaning.R....... 4 tests [0;32mOK[0m INFO [2022-04-12 23:22:16] ** 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 [2022-04-12 23:22:16] ** 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 [2022-04-12 23:22:16] ** PSMs have been aggregated to peptide ions.
test_feature_cleaning.R....... 16 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] 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 [2022-04-12 23:22:17] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2022-04-12 23:22:17] ** Features with one or two measurements across runs are removed.
test_feature_cleaning.R....... 20 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Features with one or two measurements across channels within each run are removed.
INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** Sequences containing \+ are removed.
test_filtering.R.............. 2 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** Rows with values of Symbol_1 equal to - are removed
test_filtering.R.............. 7 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values of Symbol_1 equal to +, - are removed
test_filtering.R.............. 8 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** Rows with values of Symbol_1 equal to + are removed
INFO [2022-04-12 23:22:17] ** Rows with values of Symbol_2 equal to + are removed
test_filtering.R.............. 14 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values of Symbol_1 equal to X are removed
INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 19 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 20 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 21 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 23 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 24 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 26 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Intensities with values not 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 [2022-04-12 23:22:17] ** Intensities with values not 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 [2022-04-12 23:22:17] ** Intensities with values not 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 [2022-04-12 23:22:17] ** Intensities with values not 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 [2022-04-12 23:22:17] ** Rows with values of Symbol_1 equal to + are removed
INFO [2022-04-12 23:22:17] ** Sequences containing \+ are removed.
test_filtering.R.............. 36 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Rows with values of Symbol_1 equal to + are removed
INFO [2022-04-12 23:22:17] ** Sequences containing \+ are removed.
test_filtering.R.............. 37 tests [0;32mOK[0m [0;36m78ms[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 [2022-04-12 23:22:17] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO [2022-04-12 23:22:17] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO [2022-04-12 23:22:17] ** 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;36m0ms[0m
test_shared_peptides.R........ 0 tests
test_shared_peptides.R........ 0 tests INFO [2022-04-12 23:22:17] ** Shared peptides are removed.
test_shared_peptides.R........ 0 tests
test_shared_peptides.R........ 0 tests INFO [2022-04-12 23:22:17] ** 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;36m31ms[0m
test_workflow.R............... 0 tests
test_workflow.R............... 0 tests INFO [2022-04-12 23:22:17] ** Raw data from OpenMS imported successfully.
test_workflow.R............... 0 tests
test_workflow.R............... 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Raw data from OpenMS cleaned successfully.
test_workflow.R............... 1 tests [0;32mOK[0m
test_workflow.R............... 2 tests [0;32mOK[0m INFO [2022-04-12 23:22:17] ** Using annotation extracted from quantification data.
INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** Features with all missing measurements across runs are removed.
INFO [2022-04-12 23:22:17] ** Shared peptides are removed.
INFO [2022-04-12 23:22:17] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2022-04-12 23:22:17] ** Features with one or two measurements across runs are removed.
INFO [2022-04-12 23:22:17] Proteins with a single feature are removed.
INFO [2022-04-12 23:22:17] ** 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 [2022-04-12 23:22:17] ** Features with one or two measurements across runs are removed.
INFO [2022-04-12 23:22:17] ** Fractionation handled.
INFO [2022-04-12 23:22:17] ** 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;34m0.1s[0m
All ok, 165 results (3.9s)
There were 29 warnings (use warnings() to see them)
>
>
> proc.time()
user system elapsed
3.25 0.28 4.62
|
MSstatsConvert.Rcheck/tests_x64/tinytest.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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;34m0.3s[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 [2022-04-12 23:22:19] ** Using annotation extracted from quantification data.
INFO [2022-04-12 23:22:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:19] ** Using provided annotation.
INFO [2022-04-12 23:22:19] ** 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 [2022-04-12 23:22:19] ** Using provided annotation.
INFO [2022-04-12 23:22:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 3 tests [0;32mOK[0m INFO [2022-04-12 23:22:19] ** Using provided annotation.
INFO [2022-04-12 23:22:19] ** 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 [2022-04-12 23:22:19] ** Run annotation merged with quantification data.
test_annotation.R............. 6 tests [0;32mOK[0m INFO [2022-04-12 23:22:19] ** Using provided annotation.
INFO [2022-04-12 23:22:19] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 6 tests [0;32mOK[0m INFO [2022-04-12 23:22:19] ** Run annotation merged with quantification data.
test_annotation.R............. 7 tests [0;32mOK[0m INFO [2022-04-12 23:22:19] ** Using provided annotation.
INFO [2022-04-12 23:22:19] ** 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 [2022-04-12 23:22:19] ** Using provided annotation.
INFO [2022-04-12 23:22:19] ** 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 [2022-04-12 23:22:19] ** Using provided annotation.
test_annotation.R............. 11 tests [0;32mOK[0m [0;34m0.2s[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;34m0.2s[0m
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Using selected fragments and peptides.
INFO [2022-04-12 23:22:19] ** Extracted the data from selected fragments and/or peptides.
INFO [2022-04-12 23:22:19] ** Raw data from DIAUmpire cleaned successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Using selected fragments and peptides.
INFO [2022-04-12 23:22:19] ** Extracted the data from selected fragments and/or peptides.
INFO [2022-04-12 23:22:19] ** Raw data from DIAUmpire cleaned successfully.
test_cleanRaw.R............... 0 tests INFO [2022-04-12 23:22:19] ** Using selected fragments.
INFO [2022-04-12 23:22:19] ** Extracted the data from selected fragments and/or peptides.
INFO [2022-04-12 23:22:19] ** 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 [2022-04-12 23:22:20] ** Raw data from MaxQuant imported successfully.
test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-04-12 23:22:20] ** Raw data from MaxQuant cleaned successfully.
test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Onlyidentifiedbysite equal to + are removed
INFO [2022-04-12 23:22:20] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from MaxQuant imported successfully.
test_cleanRaw.R............... 13 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2022-04-12 23:22:20] ** Rows with values of Reverse equal to + are removed
INFO [2022-04-12 23:22:20] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2022-04-12 23:22:20] ** Features with all missing measurements across channels within each run are removed.
INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from OpenMS cleaned successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m
test_cleanRaw.R............... 16 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 18 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from OpenSWATH imported successfully.
test_cleanRaw.R............... 20 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from Progenesis imported successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Progenesis imported successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Progenesis cleaned successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Skyline cleaned successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Raw data from Skyline cleaned successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from SpectroMine imported successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from SpectroMine imported successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] 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 [2022-04-12 23:22:20] ** Raw data from Spectronaut imported successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Spectronaut imported successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Raw data from Spectronaut cleaned successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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;34m1.3s[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;36m0ms[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 [2022-04-12 23:22:20] ** Features with one or two measurements across channels within each run are removed.
test_feature_cleaning.R....... 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** Features with one or two measurements across runs are removed.
test_feature_cleaning.R....... 2 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** Features with all missing measurements across runs are removed.
test_feature_cleaning.R....... 4 tests [0;32mOK[0m INFO [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** 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 [2022-04-12 23:22:20] ** PSMs have been aggregated to peptide ions.
test_feature_cleaning.R....... 16 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] 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 [2022-04-12 23:22:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2022-04-12 23:22:21] ** Features with one or two measurements across runs are removed.
test_feature_cleaning.R....... 20 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Features with one or two measurements across channels within each run are removed.
INFO [2022-04-12 23:22:21] ** 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;34m0.3s[0m
test_filtering.R.............. 0 tests
test_filtering.R.............. 0 tests
test_filtering.R.............. 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Sequences containing \+ are removed.
test_filtering.R.............. 2 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** Rows with values of Symbol_1 equal to - are removed
test_filtering.R.............. 7 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values of Symbol_1 equal to +, - are removed
test_filtering.R.............. 8 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** Rows with values of Symbol_1 equal to + are removed
INFO [2022-04-12 23:22:21] ** Rows with values of Symbol_2 equal to + are removed
test_filtering.R.............. 14 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values of Symbol_1 equal to X are removed
INFO [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 19 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 20 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 21 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 22 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 23 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 24 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 25 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 26 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Intensities with values not 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 [2022-04-12 23:22:21] ** Intensities with values not 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 [2022-04-12 23:22:21] ** Intensities with values not 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 [2022-04-12 23:22:21] ** Intensities with values not 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 [2022-04-12 23:22:21] ** Rows with values of Symbol_1 equal to + are removed
INFO [2022-04-12 23:22:21] ** Sequences containing \+ are removed.
test_filtering.R.............. 36 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Rows with values of Symbol_1 equal to + are removed
INFO [2022-04-12 23:22:21] ** Sequences containing \+ are removed.
test_filtering.R.............. 37 tests [0;32mOK[0m [0;36m47ms[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 [2022-04-12 23:22:21] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO [2022-04-12 23:22:21] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO [2022-04-12 23:22:21] ** 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;36m78ms[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;36m0ms[0m
test_shared_peptides.R........ 0 tests
test_shared_peptides.R........ 0 tests INFO [2022-04-12 23:22:21] ** Shared peptides are removed.
test_shared_peptides.R........ 0 tests
test_shared_peptides.R........ 0 tests INFO [2022-04-12 23:22:21] ** 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;36m16ms[0m
test_workflow.R............... 0 tests
test_workflow.R............... 0 tests INFO [2022-04-12 23:22:21] ** Raw data from OpenMS imported successfully.
test_workflow.R............... 0 tests
test_workflow.R............... 1 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Raw data from OpenMS cleaned successfully.
test_workflow.R............... 1 tests [0;32mOK[0m
test_workflow.R............... 2 tests [0;32mOK[0m INFO [2022-04-12 23:22:21] ** Using annotation extracted from quantification data.
INFO [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** Features with all missing measurements across runs are removed.
INFO [2022-04-12 23:22:21] ** Shared peptides are removed.
INFO [2022-04-12 23:22:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2022-04-12 23:22:21] ** Features with one or two measurements across runs are removed.
INFO [2022-04-12 23:22:21] Proteins with a single feature are removed.
INFO [2022-04-12 23:22:21] ** 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 [2022-04-12 23:22:21] ** Features with one or two measurements across runs are removed.
INFO [2022-04-12 23:22:21] ** Fractionation handled.
INFO [2022-04-12 23:22:21] ** 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;36m62ms[0m
All ok, 165 results (2.4s)
There were 29 warnings (use warnings() to see them)
>
>
> proc.time()
user system elapsed
2.98 0.26 3.25
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MSstatsConvert.Rcheck/examples_i386/MSstatsConvert-Ex.timings
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MSstatsConvert.Rcheck/examples_x64/MSstatsConvert-Ex.timings
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