Mateusz Staniak
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MSstatsConvert |
| git_branch: devel |
| git_last_commit: d3a2847 |
| git_last_commit_date: 2024-12-12 12:07:14 -0500 (Thu, 12 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 | ||||
| Package 1346/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsConvert 1.17.1 (landing page) Mateusz Staniak
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the MSstatsConvert package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MSstatsConvert |
| Version: 1.17.1 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsConvert.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MSstatsConvert_1.17.1.tar.gz |
| StartedAt: 2024-12-24 02:58:24 -0500 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 02:59:13 -0500 (Tue, 24 Dec 2024) |
| EllapsedTime: 49.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstatsConvert.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsConvert.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MSstatsConvert_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MSstatsConvert.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsConvert/DESCRIPTION' ... OK
* this is package 'MSstatsConvert' version '1.17.1'
* 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 ... WARNING
Found the following significant warnings:
Warning: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized
See 'E:/biocbuild/bbs-3.21-bioc/meat/MSstatsConvert.Rcheck/00install.out' for details.
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
.cleanRawDIANN: no visible binding for global variable 'PrecursorMz'
.cleanRawDIANN: no visible binding for global variable 'FragmentInfo'
.cleanRawDIANN: no visible binding for global variable 'FragmentIon'
.cleanRawDIANN: no visible binding for global variable 'ProductCharge'
.cleanRawDIANN: no visible binding for global variable
'PeptideSequence'
.cleanRawPhilosopher: no visible binding for global variable 'Run'
.summarizeMultiplePSMs: no visible binding for global variable 'Purity'
.summarizeMultiplePSMs: no visible binding for global variable
'PeptideProphet.Probability'
DIANNtoMSstatsFormat: no visible binding for global variable
'DetectionQValue'
DIANNtoMSstatsFormat: no visible binding for global variable
'LibPGQValue'
DIANNtoMSstatsFormat: no visible binding for global variable
'LibQValue'
DIANNtoMSstatsFormat: no visible binding for global variable
'GlobalPGQValue'
DIANNtoMSstatsFormat: no visible binding for global variable
'GlobalQValue'
SkylinetoMSstatsFormat: no visible binding for global variable
'Intensity'
SpectronauttoMSstatsFormat: no visible binding for global variable
'Intensity'
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
'PrecursorMz'
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
'FragmentInfo'
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
'FragmentIon'
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
'ProductCharge'
MSstatsClean,MSstatsDIANNFiles: no visible binding for global variable
'PeptideSequence'
MSstatsClean,MSstatsPhilosopherFiles: no visible binding for global
variable 'Run'
Undefined global functions or variables:
DetectionQValue FragmentInfo FragmentIon GlobalPGQValue GlobalQValue
Intensity LibPGQValue LibQValue PeptideProphet.Probability
PeptideSequence PrecursorMz ProductCharge Purity Run
* checking Rd files ... WARNING
prepare_Rd: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized
OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'dot-cleanRawPDMSstats.Rd':
.cleanRawPDMSstats
Code: function(msstats_object, quantification_column,
protein_id_column, sequence_column, remove_shared,
run_column = "SpectrumFile")
Docs: function(msstats_object, quantification_column,
protein_id_column, sequence_column, remove_shared)
Argument names in code not in docs:
run_column
Codoc mismatches from Rd file 'dot-cleanRawPDTMT.Rd':
.cleanRawPDTMT
Code: function(msstats_object, remove_shared = TRUE,
remove_protein_groups = TRUE, protein_id_column =
"ProteinAccessions", intensity_columns_regexp =
"Abundance", run_column = "SpectrumFile")
Docs: function(msstats_object, remove_shared = TRUE,
remove_protein_groups = TRUE, protein_id_column =
"ProteinAccessions", intensity_columns_regexp =
"Abundance")
Argument names in code not in docs:
run_column
Codoc mismatches from Rd file 'dot-validatePDTMTInputColumns.Rd':
.validatePDTMTInputColumns
Code: function(pd_input, protein_id_column, num_proteins_column,
run_column, channels)
Docs: function(pd_input, protein_id_column, num_proteins_column,
channels)
Argument names in code not in docs:
run_column
Mismatches in argument names:
Position: 4 Code: run_column Docs: channels
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-filterByPattern.Rd':
'pattern'
Documented arguments not in \usage in Rd file 'dot-filterFewMeasurements.Rd':
'features_columns'
Documented arguments not in \usage in Rd file 'dot-getFullDesign.Rd':
'`feature_column`' '`measurement_col`'
Documented arguments not in \usage in Rd file 'dot-mergeAnnotation.Rd':
'data.table'
Documented arguments not in \usage in Rd file 'dot-sharedParametersAmongConverters.Rd':
'removeFewMeasurements' 'useUniquePeptide' 'summaryforMultipleRows'
'removeProtein_with1Feature' 'removeProtein_with1Peptide'
'removeOxidationMpeptides' 'removeMpeptides' 'use_log_file' 'append'
'verbose' 'log_file_path' '...'
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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'tinytest.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
'E:/biocbuild/bbs-3.21-bioc/meat/MSstatsConvert.Rcheck/00check.log'
for details.
MSstatsConvert.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MSstatsConvert ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'MSstatsConvert' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help Warning: MSstatsConvert.Rd:3: docType '_PACKAGE' is unrecognized *** 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 Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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;36m92ms[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 [2024-12-24 02:58:58] ** Using annotation extracted from quantification data.
INFO [2024-12-24 02:58:58] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 1 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Using provided annotation.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Using provided annotation.
INFO [2024-12-24 02:58:58] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 3 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Using provided annotation.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Run annotation merged with quantification data.
test_annotation.R............. 6 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Using provided annotation.
INFO [2024-12-24 02:58:58] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
test_annotation.R............. 6 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Run annotation merged with quantification data.
test_annotation.R............. 7 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Using provided annotation.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Using provided annotation.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** 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;36m84ms[0m
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Raw data from DIAUmpire imported successfully.
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Using selected fragments and peptides.
INFO [2024-12-24 02:58:58] ** Extracted the data from selected fragments and/or peptides.
INFO [2024-12-24 02:58:58] ** Raw data from DIAUmpire cleaned successfully.
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Using selected fragments and peptides.
INFO [2024-12-24 02:58:58] ** Extracted the data from selected fragments and/or peptides.
INFO [2024-12-24 02:58:58] ** Raw data from DIAUmpire cleaned successfully.
test_cleanRaw.R............... 0 tests INFO [2024-12-24 02:58:58] ** Using selected fragments.
INFO [2024-12-24 02:58:58] ** Extracted the data from selected fragments and/or peptides.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Raw data from MaxQuant imported successfully.
test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2024-12-24 02:58:58] ** Raw data from MaxQuant cleaned successfully.
test_cleanRaw.R............... 9 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Onlyidentifiedbysite equal to + are removed
INFO [2024-12-24 02:58:58] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Raw data from MaxQuant imported successfully.
test_cleanRaw.R............... 13 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:58:58] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:58:58] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2024-12-24 02:58:58] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-24 02:58:58] ** 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 [2024-12-24 02:58:58] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2024-12-24 02:58:58] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from OpenMS cleaned successfully.
test_cleanRaw.R............... 15 tests [0;32mOK[0m
test_cleanRaw.R............... 16 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from OpenMS imported successfully.
test_cleanRaw.R............... 18 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from OpenSWATH imported successfully.
test_cleanRaw.R............... 20 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 22 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer imported successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from ProteomeDiscoverer cleaned successfully.
test_cleanRaw.R............... 25 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from Progenesis imported successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Progenesis imported successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Progenesis cleaned successfully.
test_cleanRaw.R............... 30 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Skyline imported successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Skyline cleaned successfully.
test_cleanRaw.R............... 33 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Raw data from Skyline cleaned successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from SpectroMine imported successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from SpectroMine imported successfully.
test_cleanRaw.R............... 37 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] 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 [2024-12-24 02:58:59] ** Raw data from Spectronaut imported successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Spectronaut imported successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Spectronaut cleaned successfully.
test_cleanRaw.R............... 40 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** 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
test_cleanRaw.R............... 43 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from Metamorpheus imported successfully.
test_cleanRaw.R............... 43 tests [0;32mOK[0m
test_cleanRaw.R............... 44 tests [0;32mOK[0m [0;34m0.9s[0m
test_clean_DIANN.R............ 0 tests
test_clean_DIANN.R............ 0 tests
test_clean_DIANN.R............ 0 tests INFO [2024-12-24 02:58:59] ** Raw data from DIANN cleaned successfully.
test_clean_DIANN.R............ 0 tests
test_clean_DIANN.R............ 15 tests [0;32mOK[0m INFO [2024-12-24 02:58:59] ** Raw data from DIANN cleaned successfully.
test_clean_DIANN.R............ 15 tests [0;32mOK[0m
test_clean_DIANN.R............ 30 tests [0;32mOK[0m [0;36m52ms[0m
test_clean_Metamorpheus.R..... 0 tests
test_clean_Metamorpheus.R..... 0 tests INFO [2024-12-24 02:58:59] ** Raw data from Metamorpheus cleaned successfully.
test_clean_Metamorpheus.R..... 0 tests
test_clean_Metamorpheus.R..... 1 tests [0;32mOK[0m
test_clean_Metamorpheus.R..... 2 tests [0;32mOK[0m
test_clean_Metamorpheus.R..... 3 tests [0;32mOK[0m
test_clean_Metamorpheus.R..... 4 tests [0;32mOK[0m
test_clean_Metamorpheus.R..... 5 tests [0;32mOK[0m
test_clean_Metamorpheus.R..... 6 tests [0;32mOK[0m
test_clean_Metamorpheus.R..... 7 tests [0;32mOK[0m [0;36m8ms[0m
test_clean_ProteinProspector.R 0 tests
test_clean_ProteinProspector.R 0 tests
test_clean_ProteinProspector.R 0 tests INFO [2024-12-24 02:58:59] ** Raw data from ProteinProspector cleaned successfully.
test_clean_ProteinProspector.R 3 tests [0;32mOK[0m [0;36m8ms[0m
test_clean_ProteomeDiscoverer.R 0 tests
test_clean_ProteomeDiscoverer.R 0 tests
test_clean_ProteomeDiscoverer.R 0 tests
test_clean_ProteomeDiscoverer.R 3 tests [0;32mOK[0m
test_clean_ProteomeDiscoverer.R 3 tests [0;32mOK[0m
test_clean_ProteomeDiscoverer.R 3 tests [0;32mOK[0m
test_clean_ProteomeDiscoverer.R 4 tests [0;32mOK[0m
test_clean_ProteomeDiscoverer.R 4 tests [0;32mOK[0m
test_clean_ProteomeDiscoverer.R 4 tests [0;32mOK[0m
test_clean_ProteomeDiscoverer.R 7 tests [0;32mOK[0m [0;34m0.2s[0m
test_converters_DIANNtoMSstatsFormat.R 0 tests
test_converters_DIANNtoMSstatsFormat.R 0 tests
test_converters_DIANNtoMSstatsFormat.R 0 tests
test_converters_DIANNtoMSstatsFormat.R 0 tests INFO [2024-12-24 02:58:59] ** Raw data from DIANN imported successfully.
INFO [2024-12-24 02:58:59] ** Raw data from DIANN cleaned successfully.
INFO [2024-12-24 02:58:59] ** Using provided annotation.
INFO [2024-12-24 02:58:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:58:59] ** Filtering on Global Q Value < 0.01
INFO [2024-12-24 02:58:59] ** MBR was not used to analyze the data. Now setting names and filtering
INFO [2024-12-24 02:58:59] -- Filtering on GlobalPGQValue < 0.01
INFO [2024-12-24 02:58:59] -- Filtering on GlobalQValue < 0.01
INFO [2024-12-24 02:58:59] ** 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 [2024-12-24 02:58:59] ** Sequences containing DECOY, Decoys are removed.
INFO [2024-12-24 02:58:59] ** Sequences containing \(UniMod\:35\) are removed.
INFO [2024-12-24 02:58:59] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:58:59] ** Shared peptides are removed.
INFO [2024-12-24 02:58:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:58:59] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:58:59] Proteins with a single feature are removed.
INFO [2024-12-24 02:58:59] ** Run annotation merged with quantification data.
WARN [2024-12-24 02:58:59] The following features have missing values in at least one run. AESTDDVDYIMR_2_Frag1_1,
AESTDDVDYIMR_2_Frag2_1,
AGWEAYLR_2_Frag1_1,
AGWEAYLR_2_Frag2_1,
AGWEAYLR_2_Frag3_1,
AGWEAYLR_2_Frag4_1,
AIDEQFGSLDELIK_2_Frag1_1,
AIDEQFGSLDELIK_2_Frag2_1,
AIDEQFGSLDELIK_2_Frag3_1,
AIDEQFGSLDELIK_2_Frag4_1,
AIDEQFGSLDELIK_2_Frag6_1,
AIGVLPQLIIDR_3_Frag1_1,
AIGVLPQLIIDR_3_Frag2_1,
AIGVLPQLIIDR_3_Frag3_1,
AIGVLPQLIIDR_3_Frag4_1,
AIGVLPQLIIDR_3_Frag5_1,
AIGVLPQLIIDR_3_Frag6_1,
ALSADLAAR_2_Frag1_1,
ALSADLAAR_2_Frag2_1,
ANELLINVK_1_Frag1_1,
ANELLINVK_1_Frag2_1,
ASEEGNWSK_2_Frag1_1,
ASEEGNWSK_2_Frag2_1,
ASEEGNWSK_2_Frag3_1,
ASEEGNWSK_2_Frag4_1,
ASEEGNWSK_2_Frag5_1,
ASEEGNWSK_2_Frag6_1,
ATLTDLPER_2_Frag1_1,
ATLTDLPER_2_Frag2_1,
ATLTDLPER_2_Frag4_1,
AVFNLASK_2_Frag1_1,
AVFNLASK_2_Frag2_1,
AVFNLASK_2_Frag3_1,
AVFNLASK_2_Frag4_1,
AVFNLASK_2_Frag5_1,
AVFNLASK_2_Frag6_1,
AVMC(UniMod:4)VAK_1_Frag1_1,
AVMC(UniMod:4)VAK_1_Frag2_1,
AVMC(UniMod:4)VAK_1_Frag3_1,
AVMC(UniMod:4)VAK_1_Frag4_1,
AVMC(UniMod:4)VAK_1_Frag5_1,
AVMC(UniMod:4)VAK_1_Frag6_1,
AYLDELK_2_Frag1_1,
AYLDELK_2_Frag2_1,
AYLDELK_2_Frag3_1,
AYLDELK_2_Frag4_1,
AYLDELK_2_Frag5_1,
AYLDELK_2_Frag6_1,
C(UniMod:4)DLGITGVDQVR_2_Frag1_1,
C(UniMod:4)DLGITGVDQVR_2_Frag2_1,
C(UniMod:4)DLGITGVDQVR_2_Frag3_1,
C(UniMod:4)GALLDPFELINPR_2_Frag1_1,
C(UniMod:4)GALLDPFELINPR_2_Frag3_1,
C(UniMod:4)GALLDPFELINPR_2_Frag4_1,
C(UniMod:4)GALLDPFELINPR_2_Frag5_1,
DLQENLLVLR_2_Frag2_1,
DLQENLLVLR_2_Frag3_1,
DLQENLLVLR_2_Frag6_1
INFO [2024-12-24 02:58:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:58:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_DIANNtoMSstatsFormat.R 0 tests
test_converters_DIANNtoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_DIANNtoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m89ms[0m
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests INFO [2024-12-24 02:58:59] ** Raw data from DIAUmpire imported successfully.
INFO [2024-12-24 02:58:59] ** Using selected fragments and peptides.
INFO [2024-12-24 02:58:59] ** Extracted the data from selected fragments and/or peptides.
INFO [2024-12-24 02:58:59] ** Raw data from DIAUmpire cleaned successfully.
INFO [2024-12-24 02:58:59] ** Using provided annotation.
INFO [2024-12-24 02:58:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:58:59] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, FragmentIon
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:58:59] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:58:59] ** Shared peptides are removed.
INFO [2024-12-24 02:58:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:58:59] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:58:59] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:58:59] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:58:59] ** Fractionation handled.
INFO [2024-12-24 02:58:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:58:59] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_DIAUmpiretoMSstatsFormat.R 0 tests
test_converters_DIAUmpiretoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_DIAUmpiretoMSstatsFormat.R 13 tests [0;32mOK[0m [0;34m0.1s[0m
test_converters_FragPipetoMSstatsFormat.R 0 tests
test_converters_FragPipetoMSstatsFormat.R 0 tests INFO [2024-12-24 02:58:59] ** Raw data from FragPipe imported successfully.
INFO [2024-12-24 02:58:59] ** Using annotation extracted from quantification data.
INFO [2024-12-24 02:58:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:58:59] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_FragPipetoMSstatsFormat.R 0 tests
test_converters_FragPipetoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_FragPipetoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m68ms[0m
test_converters_MaxQtoMSstatsFormat.R 0 tests
test_converters_MaxQtoMSstatsFormat.R 0 tests
test_converters_MaxQtoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from MaxQuant imported successfully.
INFO [2024-12-24 02:59:00] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:59:00] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:59:00] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-24 02:59:00] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-24 02:59:00] ** Rows with values of Onlyidentifiedbysite equal to + are removed
INFO [2024-12-24 02:59:00] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO [2024-12-24 02:59:00] ** Raw data from MaxQuant cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using provided annotation.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_MaxQtoMSstatsFormat.R 0 tests
test_converters_MaxQtoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_MaxQtoMSstatsFormat.R 13 tests [0;32mOK[0m [0;34m0.1s[0m
test_converters_MetamorpheusToMSstatsFormat.R 0 tests
test_converters_MetamorpheusToMSstatsFormat.R 0 tests
test_converters_MetamorpheusToMSstatsFormat.R 0 tests
test_converters_MetamorpheusToMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from Metamorpheus imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from Metamorpheus cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using provided annotation.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_MetamorpheusToMSstatsFormat.R 0 tests
test_converters_MetamorpheusToMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_MetamorpheusToMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m96ms[0m
test_converters_OpenMStoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from OpenMS imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from OpenMS cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using annotation extracted from quantification data.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_OpenMStoMSstatsFormat.R 0 tests
test_converters_OpenMStoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_OpenMStoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m76ms[0m
test_converters_OpenSWATHtoMSstatsFormat.R 0 tests
test_converters_OpenSWATHtoMSstatsFormat.R 0 tests
test_converters_OpenSWATHtoMSstatsFormat.R 0 tests
test_converters_OpenSWATHtoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from OpenSWATH imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from OpenSWATH cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using provided annotation.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Rows with values of decoy equal to 1 are removed
INFO [2024-12-24 02:59:00] ** Rows with values not smaller than 0.01 in m_score are removed
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_OpenSWATHtoMSstatsFormat.R 0 tests
test_converters_OpenSWATHtoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_OpenSWATHtoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m92ms[0m
test_converters_PDtoMSstatsFormat.R 0 tests
test_converters_PDtoMSstatsFormat.R 0 tests
test_converters_PDtoMSstatsFormat.R 0 tests
test_converters_PDtoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using provided annotation.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_PDtoMSstatsFormat.R 0 tests
test_converters_PDtoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_PDtoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m62ms[0m
test_converters_ProgenesistoMSstatsFormat.R 0 tests
test_converters_ProgenesistoMSstatsFormat.R 0 tests
test_converters_ProgenesistoMSstatsFormat.R 0 tests
test_converters_ProgenesistoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from Progenesis imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from Progenesis cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using provided annotation.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_ProgenesistoMSstatsFormat.R 0 tests
test_converters_ProgenesistoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_ProgenesistoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m74ms[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 0 tests
test_converters_ProteinProspectortoMSstatsTMTFormat.R 0 tests
test_converters_ProteinProspectortoMSstatsTMTFormat.R 0 tests
test_converters_ProteinProspectortoMSstatsTMTFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from ProteinProspector imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from ProteinProspector cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using provided annotation.
INFO [2024-12-24 02:59:00] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-24 02:59:00] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO [2024-12-24 02:59:00] ** Fractions belonging to same mixture have been combined.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters_ProteinProspectortoMSstatsTMTFormat.R 0 tests
test_converters_ProteinProspectortoMSstatsTMTFormat.R 1 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 2 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 3 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 4 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 5 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 6 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 7 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 8 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 9 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 10 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 11 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 12 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 13 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 13 tests [0;32mOK[0m
test_converters_ProteinProspectortoMSstatsTMTFormat.R 14 tests [0;32mOK[0m [0;34m0.3s[0m
test_converters_SkylinetoMSstatsFormat.R 0 tests
test_converters_SkylinetoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from Skyline imported successfully.
INFO [2024-12-24 02:59:00] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-24 02:59:00] ** Using annotation extracted from quantification data.
INFO [2024-12-24 02:59:00] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:00] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:00] ** Rows with values of StandardType equal to iRT are removed
INFO [2024-12-24 02:59:00] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2024-12-24 02:59:00] ** DetectionQValue not found in input columns.
INFO [2024-12-24 02:59:00] ** Sequences containing DECOY, Decoys are removed.
INFO [2024-12-24 02:59:00] ** Three isotopic preaks per feature and run are summed
INFO [2024-12-24 02:59:00] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Shared peptides are removed.
INFO [2024-12-24 02:59:00] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:00] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:00] ** Fractionation handled.
INFO [2024-12-24 02:59:00] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:00] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_SkylinetoMSstatsFormat.R 0 tests
test_converters_SkylinetoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_SkylinetoMSstatsFormat.R 13 tests [0;32mOK[0m [0;34m0.1s[0m
test_converters_SpectronauttoMSstatsFormat.R 0 tests
test_converters_SpectronauttoMSstatsFormat.R 0 tests INFO [2024-12-24 02:59:00] ** Raw data from Spectronaut imported successfully.
INFO [2024-12-24 02:59:01] ** Raw data from Spectronaut cleaned successfully.
INFO [2024-12-24 02:59:01] ** Using annotation extracted from quantification data.
INFO [2024-12-24 02:59:01] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-24 02:59:01] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-24 02:59:01] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:01] ** Shared peptides are removed.
INFO [2024-12-24 02:59:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:01] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:01] ** Run annotation merged with quantification data.
INFO [2024-12-24 02:59:01] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:01] ** Fractionation handled.
INFO [2024-12-24 02:59:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-24 02:59:01] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters_SpectronauttoMSstatsFormat.R 0 tests
test_converters_SpectronauttoMSstatsFormat.R 1 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 2 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 3 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 4 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 5 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 6 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 7 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 8 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 9 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 10 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 11 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 12 tests [0;32mOK[0m
test_converters_SpectronauttoMSstatsFormat.R 13 tests [0;32mOK[0m [0;36m72ms[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..................... 7 tests [0;32mOK[0m
test_dt.R..................... 7 tests [0;32mOK[0m
test_dt.R..................... 8 tests [0;32mOK[0m
test_dt.R..................... 8 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
test_dt.R..................... 11 tests [0;32mOK[0m [0;36m14ms[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 [2024-12-24 02:59:01] ** Features with one or two measurements across channels within each run are removed.
test_feature_cleaning.R....... 1 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Features with one or two measurements across runs are removed.
test_feature_cleaning.R....... 2 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Features with all missing measurements across runs are removed.
test_feature_cleaning.R....... 4 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** PSMs have been aggregated to peptide ions.
test_feature_cleaning.R....... 16 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] 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 [2024-12-24 02:59:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:01] ** Features with one or two measurements across runs are removed.
test_feature_cleaning.R....... 20 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Sequences containing \+ are removed.
test_filtering.R.............. 2 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Rows with values of Symbol_1 equal to - are removed
test_filtering.R.............. 7 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values of Symbol_1 equal to +, - are removed
test_filtering.R.............. 8 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Rows with values of Symbol_1 equal to + are removed
INFO [2024-12-24 02:59:01] ** Rows with values of Symbol_2 equal to + are removed
test_filtering.R.............. 14 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values of Symbol_1 equal to X are removed
INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 19 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 20 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 21 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not greater than 0.3 in Score are removed
test_filtering.R.............. 22 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 23 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 24 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 25 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values not smaller than 0.3 in Score are removed
test_filtering.R.............. 26 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Rows with values of Symbol_1 equal to + are removed
INFO [2024-12-24 02:59:01] ** Sequences containing \+ are removed.
test_filtering.R.............. 36 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Rows with values of Symbol_1 equal to + are removed
INFO [2024-12-24 02:59:01] ** Sequences containing \+ are removed.
test_filtering.R.............. 37 tests [0;32mOK[0m [0;36m36ms[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 [2024-12-24 02:59:01] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO [2024-12-24 02:59:01] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal summation abundance.
INFO [2024-12-24 02:59:01] ** 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;36m70ms[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;36m2ms[0m
test_shared_peptides.R........ 0 tests
test_shared_peptides.R........ 0 tests INFO [2024-12-24 02:59:01] ** Shared peptides are removed.
test_shared_peptides.R........ 0 tests
test_shared_peptides.R........ 0 tests INFO [2024-12-24 02:59:01] ** 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;36m22ms[0m
test_workflow.R............... 0 tests
test_workflow.R............... 0 tests INFO [2024-12-24 02:59:01] ** Raw data from OpenMS imported successfully.
test_workflow.R............... 0 tests
test_workflow.R............... 1 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Raw data from OpenMS cleaned successfully.
test_workflow.R............... 1 tests [0;32mOK[0m
test_workflow.R............... 2 tests [0;32mOK[0m INFO [2024-12-24 02:59:01] ** Using annotation extracted from quantification data.
INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Features with all missing measurements across runs are removed.
INFO [2024-12-24 02:59:01] ** Shared peptides are removed.
INFO [2024-12-24 02:59:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-24 02:59:01] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:01] Proteins with a single feature are removed.
INFO [2024-12-24 02:59:01] ** 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 [2024-12-24 02:59:01] ** Features with one or two measurements across runs are removed.
INFO [2024-12-24 02:59:01] ** Fractionation handled.
INFO [2024-12-24 02:59:01] ** 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;36m57ms[0m
All ok, 371 results (3.4s)
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> proc.time()
user system elapsed
3.56 0.31 3.96
MSstatsConvert.Rcheck/MSstatsConvert-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsFormat | 0.12 | 0.02 | 0.14 | |
| DIAUmpiretoMSstatsFormat | 0.13 | 0.00 | 0.13 | |
| FragPipetoMSstatsFormat | 0.11 | 0.00 | 0.11 | |
| MSstatsBalancedDesign | 0.02 | 0.00 | 0.02 | |
| MSstatsClean | 0.15 | 0.01 | 0.21 | |
| MSstatsImport | 0.24 | 0.00 | 0.24 | |
| MSstatsLogsSettings | 0.03 | 0.00 | 0.03 | |
| MSstatsMakeAnnotation | 0.23 | 0.00 | 0.25 | |
| MSstatsPreprocess | 0.19 | 0.00 | 0.18 | |
| MSstatsSaveSessionInfo | 0.03 | 0.00 | 0.03 | |
| MaxQtoMSstatsFormat | 0.14 | 0.04 | 0.19 | |
| MetamorpheusToMSstatsFormat | 0.06 | 0.01 | 0.08 | |
| OpenMStoMSstatsFormat | 0.08 | 0.00 | 0.08 | |
| OpenSWATHtoMSstatsFormat | 0.11 | 0.00 | 0.11 | |
| PDtoMSstatsFormat | 0.09 | 0.00 | 0.09 | |
| ProgenesistoMSstatsFormat | 0.08 | 0.02 | 0.10 | |
| ProteinProspectortoMSstatsTMTFormat | 0.24 | 0.03 | 0.26 | |
| SkylinetoMSstatsFormat | 0.09 | 0.01 | 0.11 | |
| SpectronauttoMSstatsFormat | 0.06 | 0.00 | 0.06 | |
| getDataType | 0.16 | 0.00 | 0.16 | |
| getInputFile | 0.20 | 0.02 | 0.22 | |