Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1355/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstatsPTM 2.8.1 (landing page) Devon Kohler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the MSstatsPTM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.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: MSstatsPTM |
Version: 2.8.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.8.1.tar.gz |
StartedAt: 2024-12-20 06:37:00 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:44:38 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 457.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSstatsPTM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsPTM’ version ‘2.8.1’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MSstatsPTM’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘MSstats:::.getMedianSigmaSubject’ ‘MSstats:::.getVarComponent’ ‘MSstatsConvert:::.filterFewMeasurements’ ‘MSstatsConvert:::.filterManyColumns’ ‘MSstatsConvert:::.getChannelColumns’ ‘MSstatsConvert:::.standardizeColnames’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .extract_pd_mods: no visible binding for global variable ‘..sequence_col’ .format.data.process.plots: no visible binding for global variable ‘ABUNDANCE’ .pivotPS: no visible binding for global variable ‘..keep_cols’ .plot.model.volcano: no visible binding for global variable ‘text.angle’ .progensis.add.sites: no visible binding for global variable ‘..col_order’ .qc.all.plot.lf: no visible binding for global variable ‘text.angle’ .qc.single.plot.lf: no visible binding for global variable ‘text.angle’ .removeCutoffSites: no visible binding for global variable ‘..mod_pep_col’ .rmConfounded: no visible binding for global variable ‘..col_res’ DIANNtoMSstatsPTMFormat: no visible binding for global variable ‘..protein_id_col’ FragPipetoMSstatsPTMFormat: no visible binding for global variable ‘..msstats_cols’ MSstatsPTMSiteLocator: no visible binding for global variable ‘..mod_pep_col’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘TMT.keyword’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘ptm.keyword’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘mod.num’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘which.proteinid.ptm’ MaxQtoMSstatsPTMFormat: no visible binding for global variable ‘PeptideSequence’ MetamorpheusToMSstatsPTMFormat: no visible binding for global variable ‘..protein_id_col’ PStoMSstatsPTMFormat: no visible binding for global variable ‘Intensity’ ProgenesistoMSstatsPTMFormat: no visible binding for global variable ‘Type’ SkylinetoMSstatsPTMFormat: no visible binding for global variable ‘annotation_prot’ dataProcessPlotsPTM: no visible binding for global variable ‘PROTEINNAME’ dataProcessPlotsPTM: no visible binding for global variable ‘GLOBALPROTEIN’ dataSummarizationPTM: no visible binding for global variable ‘address’ locatePTM: no visible binding for global variable ‘..col_seq’ locatePTM: no visible binding for global variable ‘..col_fasta’ Undefined global functions or variables: ..col_fasta ..col_order ..col_res ..col_seq ..keep_cols ..mod_pep_col ..msstats_cols ..protein_id_col ..sequence_col ABUNDANCE GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence TMT.keyword Type address annotation_prot mod.num ptm.keyword text.angle which.proteinid.ptm * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'dot-fixTerminus.Rd': ‘fasta_file’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed groupComparisonPlotsPTM 26.120 0.142 28.455 groupComparisonPTM 9.890 0.093 9.926 designSampleSizePTM 9.791 0.119 10.034 dataSummarizationPTM_TMT 9.162 0.222 11.017 dataProcessPlotsPTM 5.461 0.049 6.153 dataSummarizationPTM 4.590 0.096 5.082 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck/00check.log’ for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MSstatsPTM’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c model_adjustment.cpp -o model_adjustment.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsPTM)
MSstatsPTM.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(mockery) > library(MSstatsPTM) > > test_check("MSstatsPTM") Drew the Quality Contol plot(boxplot) for all ptms/proteins. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 12.714 0.841 13.799
MSstatsPTM.Rcheck/tests/tinytest.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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) ){ + tinytest::test_package("MSstatsPTM") + } test_converters.R............. 0 tests test_converters.R............. 0 tests test_converters.R............. 0 tests test_converters.R............. 0 tests test_converters.R............. 0 tests test_converters.R............. 1 tests [0;32mOK[0m test_converters.R............. 2 tests [0;32mOK[0m test_converters.R............. 3 tests [0;32mOK[0m test_converters.R............. 4 tests [0;32mOK[0m test_converters.R............. 5 tests [0;32mOK[0m INFO [2024-12-20 06:43:15] ** Raw data from MaxQuant imported successfully. INFO [2024-12-20 06:43:15] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2024-12-20 06:43:15] ** Rows with values of Reverse equal to + are removed INFO [2024-12-20 06:43:15] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:15] ** Using provided annotation. INFO [2024-12-20 06:43:15] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:15] ** 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 kept. INFO [2024-12-20 06:43:15] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:15] ** Shared peptides are removed. INFO [2024-12-20 06:43:15] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:15] ** PSMs have been aggregated to peptide ions. INFO [2024-12-20 06:43:15] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:15] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:15] ** Fractionation handled. INFO [2024-12-20 06:43:15] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:15] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. test_converters.R............. 5 tests [0;32mOK[0m test_converters.R............. 7 tests [0;32mOK[0m test_converters.R............. 8 tests [0;32mOK[0m test_converters.R............. 9 tests [0;32mOK[0m test_converters.R............. 10 tests [0;32mOK[0m test_converters.R............. 11 tests [0;32mOK[0m test_converters.R............. 12 tests [0;32mOK[0m test_converters.R............. 12 tests [0;32mOK[0m test_converters.R............. 12 tests [0;32mOK[0m test_converters.R............. 13 tests [0;32mOK[0m test_converters.R............. 14 tests [0;32mOK[0m test_converters.R............. 15 tests [0;32mOK[0m test_converters.R............. 16 tests [0;32mOK[0m test_converters.R............. 17 tests [0;32mOK[0m INFO [2024-12-20 06:43:16] ** Raw data from MaxQuant imported successfully. INFO [2024-12-20 06:43:16] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2024-12-20 06:43:16] ** Rows with values of Reverse equal to + are removed INFO [2024-12-20 06:43:16] ** Using provided annotation. INFO [2024-12-20 06:43:16] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:16] ** 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 [2024-12-20 06:43:16] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:16] ** Shared peptides are removed. INFO [2024-12-20 06:43:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:16] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:16] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:16] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:16] ** Fractionation handled. INFO [2024-12-20 06:43:16] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:16] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 17 tests [0;32mOK[0m test_converters.R............. 19 tests [0;32mOK[0m test_converters.R............. 20 tests [0;32mOK[0m test_converters.R............. 21 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 23 tests [0;32mOK[0m test_converters.R............. 24 tests [0;32mOK[0m test_converters.R............. 24 tests [0;32mOK[0m test_converters.R............. 24 tests [0;32mOK[0m test_converters.R............. 25 tests [0;32mOK[0m test_converters.R............. 26 tests [0;32mOK[0m test_converters.R............. 27 tests [0;32mOK[0m test_converters.R............. 28 tests [0;32mOK[0m INFO [2024-12-20 06:43:23] ** Raw data from Spectronaut imported successfully. INFO [2024-12-20 06:43:23] ** Raw data from Spectronaut cleaned successfully. INFO [2024-12-20 06:43:23] ** Using provided annotation. INFO [2024-12-20 06:43:23] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:23] ** 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. WARN [2024-12-20 06:43:23] ** PGQvalue not found in input columns. WARN [2024-12-20 06:43:23] ** EGQvalue not found in input columns. INFO [2024-12-20 06:43:23] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:23] ** Shared peptides are removed. INFO [2024-12-20 06:43:23] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:23] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:23] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:23] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:23] ** Fractionation handled. INFO [2024-12-20 06:43:23] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:23] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 28 tests [0;32mOK[0m test_converters.R............. 30 tests [0;32mOK[0m test_converters.R............. 31 tests [0;32mOK[0m test_converters.R............. 32 tests [0;32mOK[0m test_converters.R............. 33 tests [0;32mOK[0m test_converters.R............. 34 tests [0;32mOK[0m test_converters.R............. 35 tests [0;32mOK[0m test_converters.R............. 35 tests [0;32mOK[0m test_converters.R............. 35 tests [0;32mOK[0m test_converters.R............. 35 tests [0;32mOK[0m INFO [2024-12-20 06:43:25] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:25] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:25] ** Using provided annotation. INFO [2024-12-20 06:43:25] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:25] ** 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 [2024-12-20 06:43:26] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:26] ** Shared peptides are removed. INFO [2024-12-20 06:43:26] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:26] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:26] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:26] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:26] ** Fractionation handled. INFO [2024-12-20 06:43:26] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:26] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 36 tests [0;32mOK[0m INFO: Extracting modifications INFO [2024-12-20 06:43:28] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:28] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:28] ** Using provided annotation. INFO [2024-12-20 06:43:28] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:28] ** 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 [2024-12-20 06:43:28] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:28] ** Shared peptides are removed. INFO [2024-12-20 06:43:28] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:28] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:28] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:28] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:28] ** Fractionation handled. INFO [2024-12-20 06:43:28] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:28] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 37 tests [0;32mOK[0m INFO: Extracting modifications INFO [2024-12-20 06:43:30] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:30] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:30] ** Using provided annotation. INFO [2024-12-20 06:43:30] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:30] ** 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 [2024-12-20 06:43:30] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:30] ** Shared peptides are removed. INFO [2024-12-20 06:43:30] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:30] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:30] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:30] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:30] ** Fractionation handled. INFO [2024-12-20 06:43:30] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:30] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 38 tests [0;32mOK[0m INFO [2024-12-20 06:43:32] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:32] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:32] ** Using provided annotation. INFO [2024-12-20 06:43:32] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:32] ** 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 [2024-12-20 06:43:32] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:32] ** Shared peptides are removed. INFO [2024-12-20 06:43:32] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:32] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:32] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:32] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:32] ** Fractionation handled. INFO [2024-12-20 06:43:32] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:32] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 39 tests [0;32mOK[0m test_converters.R............. 40 tests [0;32mOK[0m INFO [2024-12-20 06:43:34] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:34] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:34] ** Using provided annotation. INFO [2024-12-20 06:43:34] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:34] ** 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 [2024-12-20 06:43:34] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:34] ** Shared peptides are removed. INFO [2024-12-20 06:43:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:34] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:34] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:34] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:34] ** Fractionation handled. INFO [2024-12-20 06:43:35] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:35] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 41 tests [0;32mOK[0m test_converters.R............. 42 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 43 tests [0;32mOK[0m INFO: Extracting modifications INFO [2024-12-20 06:43:35] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:35] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:35] ** Using provided annotation. INFO [2024-12-20 06:43:35] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:35] ** 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 [2024-12-20 06:43:35] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:35] ** Shared peptides are removed. INFO [2024-12-20 06:43:35] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:35] ** PSMs have been aggregated to peptide ions. INFO [2024-12-20 06:43:35] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:35] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:35] ** Fractionation handled. INFO [2024-12-20 06:43:35] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:35] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. INFO [2024-12-20 06:43:35] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-12-20 06:43:35] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-12-20 06:43:35] ** Using provided annotation. INFO [2024-12-20 06:43:35] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:35] ** 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 [2024-12-20 06:43:35] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:35] ** Shared peptides are removed. INFO [2024-12-20 06:43:35] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:35] ** PSMs have been aggregated to peptide ions. INFO [2024-12-20 06:43:35] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:35] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance. INFO [2024-12-20 06:43:35] ** Fractions belonging to same mixture have been combined. INFO [2024-12-20 06:43:35] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:35] ** Fractionation handled. INFO [2024-12-20 06:43:35] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:35] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. test_converters.R............. 43 tests [0;32mOK[0m test_converters.R............. 45 tests [0;32mOK[0m test_converters.R............. 46 tests [0;32mOK[0m test_converters.R............. 47 tests [0;32mOK[0m test_converters.R............. 48 tests [0;32mOK[0m test_converters.R............. 49 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 50 tests [0;32mOK[0m test_converters.R............. 51 tests [0;32mOK[0m test_converters.R............. 52 tests [0;32mOK[0m test_converters.R............. 53 tests [0;32mOK[0m test_converters.R............. 54 tests [0;32mOK[0m test_converters.R............. 55 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus imported successfully. INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-12-20 06:43:36] ** Using provided annotation. INFO [2024-12-20 06:43:36] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:36] ** 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 [2024-12-20 06:43:36] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Shared peptides are removed. INFO [2024-12-20 06:43:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Fractionation handled. INFO [2024-12-20 06:43:36] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus imported successfully. INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-12-20 06:43:36] ** Using provided annotation. INFO [2024-12-20 06:43:36] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:36] ** 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 [2024-12-20 06:43:36] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Shared peptides are removed. INFO [2024-12-20 06:43:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Fractionation handled. INFO [2024-12-20 06:43:36] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 55 tests [0;32mOK[0m test_converters.R............. 57 tests [0;32mOK[0m test_converters.R............. 58 tests [0;32mOK[0m test_converters.R............. 59 tests [0;32mOK[0m test_converters.R............. 60 tests [0;32mOK[0m test_converters.R............. 61 tests [0;32mOK[0m test_converters.R............. 62 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus imported successfully. INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-12-20 06:43:36] ** Using provided annotation. INFO [2024-12-20 06:43:36] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:36] ** 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 [2024-12-20 06:43:36] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Shared peptides are removed. INFO [2024-12-20 06:43:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Fractionation handled. INFO [2024-12-20 06:43:36] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus imported successfully. INFO [2024-12-20 06:43:36] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-12-20 06:43:36] ** Using provided annotation. INFO [2024-12-20 06:43:36] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:36] ** 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 [2024-12-20 06:43:36] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Shared peptides are removed. INFO [2024-12-20 06:43:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:36] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:36] ** Fractionation handled. INFO [2024-12-20 06:43:36] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 62 tests [0;32mOK[0m test_converters.R............. 64 tests [0;32mOK[0m test_converters.R............. 65 tests [0;32mOK[0m test_converters.R............. 66 tests [0;32mOK[0m test_converters.R............. 67 tests [0;32mOK[0m test_converters.R............. 68 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 69 tests [0;32mOK[0m test_converters.R............. 70 tests [0;32mOK[0m test_converters.R............. 71 tests [0;32mOK[0m INFO [2024-12-20 06:43:37] ** Raw data from Progenesis imported successfully. INFO [2024-12-20 06:43:37] ** Raw data from Progenesis cleaned successfully. INFO [2024-12-20 06:43:37] ** Using provided annotation. INFO [2024-12-20 06:43:37] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:37] ** 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 [2024-12-20 06:43:37] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:37] ** Shared peptides are removed. INFO [2024-12-20 06:43:37] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 06:43:37] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:37] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:37] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 06:43:37] ** Fractionation handled. INFO [2024-12-20 06:43:37] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:37] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 71 tests [0;32mOK[0m test_converters.R............. 72 tests [0;32mOK[0m test_converters.R............. 73 tests [0;32mOK[0m test_converters.R............. 74 tests [0;32mOK[0m INFO [2024-12-20 06:43:39] ** Raw data from Philosopher imported successfully. INFO [2024-12-20 06:43:39] ** Using provided annotation. INFO [2024-12-20 06:43:39] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:39] ** 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 kept. INFO [2024-12-20 06:43:39] ** Rows with values not greater than 0.6 in Purity are removed WARN [2024-12-20 06:43:39] ** PeptideProphetProbability not found in input columns. INFO [2024-12-20 06:43:39] ** Sequences containing Oxidation are removed. INFO [2024-12-20 06:43:39] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:39] ** Shared peptides are removed. INFO [2024-12-20 06:43:39] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:39] ** PSMs have been aggregated to peptide ions. INFO [2024-12-20 06:43:39] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:39] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:39] ** Fractionation handled. INFO [2024-12-20 06:43:39] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:39] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. INFO [2024-12-20 06:43:39] ** Raw data from Philosopher imported successfully. test_converters.R............. 75 tests [0;32mOK[0m test_converters.R............. 76 tests [0;32mOK[0m INFO [2024-12-20 06:43:40] ** Raw data from Philosopher imported successfully. INFO [2024-12-20 06:43:40] ** Using provided annotation. INFO [2024-12-20 06:43:40] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:40] ** 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 kept. INFO [2024-12-20 06:43:40] ** Rows with values not greater than 0.6 in Purity are removed WARN [2024-12-20 06:43:40] ** PeptideProphetProbability not found in input columns. INFO [2024-12-20 06:43:40] ** Sequences containing Oxidation are removed. INFO [2024-12-20 06:43:40] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:40] ** Shared peptides are removed. INFO [2024-12-20 06:43:40] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:40] ** PSMs have been aggregated to peptide ions. INFO [2024-12-20 06:43:40] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:40] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:40] ** Fractionation handled. INFO [2024-12-20 06:43:40] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:40] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. INFO [2024-12-20 06:43:40] ** Raw data from Philosopher imported successfully. INFO [2024-12-20 06:43:40] ** Using provided annotation. INFO [2024-12-20 06:43:40] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:40] ** 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 kept. INFO [2024-12-20 06:43:40] ** Rows with values not greater than 0.6 in Purity are removed WARN [2024-12-20 06:43:40] ** PeptideProphetProbability not found in input columns. INFO [2024-12-20 06:43:40] ** Sequences containing Oxidation are removed. INFO [2024-12-20 06:43:40] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:40] ** Shared peptides are removed. INFO [2024-12-20 06:43:40] ** Features with all missing measurements across channels within each run are removed. INFO [2024-12-20 06:43:40] ** PSMs have been aggregated to peptide ions. INFO [2024-12-20 06:43:40] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:40] ** Features with one or two measurements across channels within each run are removed. INFO [2024-12-20 06:43:40] ** Fractionation handled. INFO [2024-12-20 06:43:40] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:40] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. test_converters.R............. 76 tests [0;32mOK[0m test_converters.R............. 78 tests [0;32mOK[0m test_converters.R............. 79 tests [0;32mOK[0m test_converters.R............. 80 tests [0;32mOK[0m test_converters.R............. 81 tests [0;32mOK[0m test_converters.R............. 82 tests [0;32mOK[0m test_converters.R............. 83 tests [0;32mOK[0m test_converters.R............. 83 tests [0;32mOK[0m test_converters.R............. 83 tests [0;32mOK[0m test_converters.R............. 83 tests [0;32mOK[0m test_converters.R............. 83 tests [0;32mOK[0m test_converters.R............. 84 tests [0;32mOK[0m test_converters.R............. 85 tests [0;32mOK[0m INFO [2024-12-20 06:43:41] ** Raw data from FragPipe imported successfully. INFO [2024-12-20 06:43:41] ** Using annotation extracted from quantification data. INFO [2024-12-20 06:43:41] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 06:43:41] ** 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 kept. INFO [2024-12-20 06:43:41] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:41] ** Shared peptides are removed. INFO [2024-12-20 06:43:41] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum INFO [2024-12-20 06:43:41] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:41] ** Run annotation merged with quantification data. INFO [2024-12-20 06:43:41] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 06:43:41] ** Fractionation handled. INFO [2024-12-20 06:43:41] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 06:43:41] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 85 tests [0;32mOK[0m test_converters.R............. 86 tests [0;32mOK[0m test_converters.R............. 87 tests [0;32mOK[0m test_converters.R............. 88 tests [0;32mOK[0m [0;34m27.9s[0m test_dataSummarizationPTM.R... 0 tests test_dataSummarizationPTM.R... 1 tests [0;32mOK[0m test_dataSummarizationPTM.R... 2 tests [0;32mOK[0m test_dataSummarizationPTM.R... 3 tests [0;32mOK[0m test_dataSummarizationPTM.R... 4 tests [0;32mOK[0m test_dataSummarizationPTM.R... 5 tests [0;32mOK[0m test_dataSummarizationPTM.R... 6 tests [0;32mOK[0m test_dataSummarizationPTM.R... 7 tests [0;32mOK[0m test_dataSummarizationPTM.R... 8 tests [0;32mOK[0m test_dataSummarizationPTM.R... 9 tests [0;32mOK[0m test_dataSummarizationPTM.R... 10 tests [0;32mOK[0m test_dataSummarizationPTM.R... 11 tests [0;32mOK[0m test_dataSummarizationPTM.R... 12 tests [0;32mOK[0m test_dataSummarizationPTM.R... 13 tests [0;32mOK[0m test_dataSummarizationPTM.R... 14 tests [0;32mOK[0m test_dataSummarizationPTM.R... 15 tests [0;32mOK[0m test_dataSummarizationPTM.R... 16 tests [0;32mOK[0m test_dataSummarizationPTM.R... 17 tests [0;32mOK[0m test_dataSummarizationPTM.R... 18 tests [0;32mOK[0m test_dataSummarizationPTM.R... 19 tests [0;32mOK[0m test_dataSummarizationPTM.R... 20 tests [0;32mOK[0m test_dataSummarizationPTM.R... 21 tests [0;32mOK[0m test_dataSummarizationPTM.R... 22 tests [0;32mOK[0m test_dataSummarizationPTM.R... 23 tests [0;32mOK[0m test_dataSummarizationPTM.R... 24 tests [0;32mOK[0m test_dataSummarizationPTM.R... 25 tests [0;32mOK[0m test_dataSummarizationPTM.R... 26 tests [0;32mOK[0m test_dataSummarizationPTM.R... 27 tests [0;32mOK[0m test_dataSummarizationPTM.R... 28 tests [0;32mOK[0m test_dataSummarizationPTM.R... 29 tests [0;32mOK[0m test_dataSummarizationPTM.R... 30 tests [0;32mOK[0m Starting PTM summarization... test_dataSummarizationPTM.R... 31 tests [0;32mOK[0m [0;34m0.9s[0m test_dataSummarizationPTM_TMT.R 0 tests test_dataSummarizationPTM_TMT.R 1 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 2 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 3 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 4 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 5 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 6 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 7 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 8 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 9 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 10 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 11 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 12 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 13 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 14 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 15 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 16 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 17 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 18 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 19 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 20 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 21 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 22 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 23 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 24 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 25 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 26 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 27 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 28 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 29 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 30 tests [0;32mOK[0m test_dataSummarizationPTM_TMT.R 31 tests [0;32mOK[0m [0;34m0.6s[0m test_groupComparisonPTM.R..... 0 tests test_groupComparisonPTM.R..... 0 tests test_groupComparisonPTM.R..... 1 tests [0;32mOK[0m test_groupComparisonPTM.R..... 2 tests [0;32mOK[0m Starting PTM modeling... test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m Starting PTM modeling... INFO [2024-12-20 06:43:52] == Start to test and get inference in whole plot ... | | | 0% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |============== | 21% | |=============== | 21% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 26% | |=================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |===================== | 31% | |====================== | 31% | |======================= | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================== | 42% | |============================== | 43% | |=============================== | 44% | |=============================== | 45% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 55% | |======================================= | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 69% | |================================================= | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |=================================================== | 74% | |==================================================== | 74% | |===================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 79% | |======================================================== | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% INFO [2024-12-20 06:44:00] == Comparisons for all proteins are done. Starting Protein modeling... INFO [2024-12-20 06:44:00] == Start to test and get inference in whole plot ... | | | 0% | |=== | 4% | |===== | 8% | |======== | 12% | |=========== | 15% | |============= | 19% | |================ | 23% | |=================== | 27% | |====================== | 31% | |======================== | 35% | |=========================== | 38% | |============================== | 42% | |================================ | 46% | |=================================== | 50% | |====================================== | 54% | |======================================== | 58% | |=========================================== | 62% | |============================================== | 65% | |================================================ | 69% | |=================================================== | 73% | |====================================================== | 77% | |========================================================= | 81% | |=========================================================== | 85% | |============================================================== | 88% | |================================================================= | 92% | |=================================================================== | 96% | |======================================================================| 100% INFO [2024-12-20 06:44:02] == Comparisons for all proteins are done. Starting adjustment... test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m test_groupComparisonPTM.R..... 4 tests [0;32mOK[0m test_groupComparisonPTM.R..... 5 tests [0;32mOK[0m test_groupComparisonPTM.R..... 6 tests [0;32mOK[0m test_groupComparisonPTM.R..... 7 tests [0;32mOK[0m test_groupComparisonPTM.R..... 8 tests [0;32mOK[0m test_groupComparisonPTM.R..... 9 tests [0;32mOK[0m test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m Starting PTM modeling... INFO [2024-12-20 06:44:02] Design: 2 mixtures. INFO [2024-12-20 06:44:02] Design: 1 MS run per mixture. INFO [2024-12-20 06:44:02] Design: group comparison design (Different conditions contains different biological subjects). INFO [2024-12-20 06:44:02] Model fitting for 90 proteins. | | | 0% | |= | 1% | |== | 2% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |========= | 12% | |========= | 13% | |========== | 14% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |================ | 22% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |======================= | 32% | |======================= | 33% | |======================== | 34% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================== | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |=================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% INFO [2024-12-20 06:44:07] Testing for 90 proteins: | | | 0% | |= | 1% | |== | 2% | |== | 3% | |=== | 4% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |========= | 12% | |========= | 13% | |========== | 14% | |=========== | 16% | |============ | 17% | |============ | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |================ | 22% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |======================= | 32% | |======================= | 33% | |======================== | 34% | |========================= | 36% | |========================== | 37% | |========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================== | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 46% | |================================= | 47% | |================================= | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |===================================== | 52% | |===================================== | 53% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |======================================== | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 66% | |=============================================== | 67% | |=============================================== | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |=================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |===================================================== | 76% | |====================================================== | 77% | |====================================================== | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 86% | |============================================================= | 87% | |============================================================= | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================= | 92% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 96% | |==================================================================== | 97% | |==================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Starting Protein modeling... INFO [2024-12-20 06:44:08] Design: 2 mixtures. INFO [2024-12-20 06:44:08] Design: 1 MS run per mixture. INFO [2024-12-20 06:44:08] Design: group comparison design (Different conditions contains different biological subjects). INFO [2024-12-20 06:44:08] Model fitting for 85 proteins. | | | 0% | |= | 1% | |== | 2% | |== | 4% | |=== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |======= | 9% | |======= | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |=========== | 15% | |============ | 16% | |============ | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |================ | 22% | |================ | 24% | |================= | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |===================== | 29% | |===================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |========================= | 35% | |========================== | 36% | |========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================== | 42% | |============================== | 44% | |=============================== | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |=================================== | 49% | |=================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |======================================= | 55% | |======================================== | 56% | |======================================== | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 62% | |============================================ | 64% | |============================================= | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================= | 69% | |================================================= | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |===================================================== | 75% | |====================================================== | 76% | |====================================================== | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 82% | |========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |=============================================================== | 89% | |=============================================================== | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 95% | |==================================================================== | 96% | |==================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% INFO [2024-12-20 06:44:20] Testing for 85 proteins: | | | 0% | |= | 1% | |== | 2% | |== | 4% | |=== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |======= | 9% | |======= | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |=========== | 15% | |============ | 16% | |============ | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |================ | 22% | |================ | 24% | |================= | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |===================== | 29% | |===================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |========================= | 35% | |========================== | 36% | |========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================== | 42% | |============================== | 44% | |=============================== | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |=================================== | 49% | |=================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |======================================= | 55% | |======================================== | 56% | |======================================== | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |============================================ | 62% | |============================================ | 64% | |============================================= | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================= | 69% | |================================================= | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |===================================================== | 75% | |====================================================== | 76% | |====================================================== | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 82% | |========================================================== | 84% | |=========================================================== | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |=============================================================== | 89% | |=============================================================== | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |=================================================================== | 95% | |==================================================================== | 96% | |==================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Starting adjustment... test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m test_groupComparisonPTM.R..... 11 tests [0;32mOK[0m test_groupComparisonPTM.R..... 12 tests [0;32mOK[0m test_groupComparisonPTM.R..... 13 tests [0;32mOK[0m test_groupComparisonPTM.R..... 14 tests [0;32mOK[0m test_groupComparisonPTM.R..... 15 tests [0;32mOK[0m test_groupComparisonPTM.R..... 16 tests [0;32mOK[0m test_groupComparisonPTM.R..... 17 tests [0;32mOK[0m [0;34m38.9s[0m All ok, 167 results (1m 8.4s) There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 75.707 2.409 81.087
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
name | user | system | elapsed | |
DIANNtoMSstatsPTMFormat | 0.000 | 0.001 | 0.001 | |
FragPipetoMSstatsPTMFormat | 1.754 | 0.099 | 2.031 | |
MSstatsPTMSiteLocator | 0.001 | 0.000 | 0.000 | |
MaxQtoMSstatsPTMFormat | 0.995 | 0.096 | 0.960 | |
MetamorpheusToMSstatsPTMFormat | 0.346 | 0.037 | 0.328 | |
PDtoMSstatsPTMFormat | 2.487 | 0.211 | 2.698 | |
PStoMSstatsPTMFormat | 0.153 | 0.009 | 0.157 | |
ProgenesistoMSstatsPTMFormat | 0.143 | 0.014 | 0.158 | |
SkylinetoMSstatsPTMFormat | 0.107 | 0.002 | 0.112 | |
SpectronauttoMSstatsPTMFormat | 1.480 | 0.070 | 1.539 | |
annotSite | 0.001 | 0.000 | 0.001 | |
dataProcessPlotsPTM | 5.461 | 0.049 | 6.153 | |
dataSummarizationPTM | 4.590 | 0.096 | 5.082 | |
dataSummarizationPTM_TMT | 9.162 | 0.222 | 11.017 | |
designSampleSizePTM | 9.791 | 0.119 | 10.034 | |
fragpipe_annotation | 0.003 | 0.002 | 0.006 | |
fragpipe_annotation_protein | 0.004 | 0.002 | 0.005 | |
fragpipe_input | 0.013 | 0.005 | 0.017 | |
fragpipe_input_protein | 0.012 | 0.003 | 0.015 | |
groupComparisonPTM | 9.890 | 0.093 | 9.926 | |
groupComparisonPlotsPTM | 26.120 | 0.142 | 28.455 | |
locateMod | 0.001 | 0.001 | 0.001 | |
locatePTM | 0.028 | 0.003 | 0.032 | |
maxq_lf_annotation | 0.003 | 0.002 | 0.005 | |
maxq_lf_evidence | 0.026 | 0.010 | 0.036 | |
maxq_tmt_annotation | 0.004 | 0.001 | 0.005 | |
maxq_tmt_evidence | 0.041 | 0.013 | 0.055 | |
pd_annotation | 0.002 | 0.000 | 0.003 | |
pd_psm_input | 0.028 | 0.009 | 0.037 | |
pd_testing_output | 0.305 | 0.470 | 0.786 | |
raw.input | 0.106 | 0.001 | 0.108 | |
raw.input.tmt | 0.011 | 0.003 | 0.014 | |
spectronaut_annotation | 0.003 | 0.001 | 0.005 | |
spectronaut_input | 0.010 | 0.003 | 0.013 | |
summary.data | 0.665 | 1.201 | 1.883 | |
summary.data.tmt | 1.299 | 2.281 | 3.628 | |
tidyFasta | 0.015 | 0.002 | 0.017 | |