Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 1385/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstatsPTM 2.10.1 (landing page) Devon Kohler
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2.10.1 |
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_2.10.1.tar.gz |
StartedAt: 2025-08-01 06:52:10 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 06:57:36 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 325.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MSstatsPTM.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_2.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsPTM.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * 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 ‘2.10.1’ * 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 ... ERROR Running examples in ‘MSstatsPTM-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MetamorpheusToMSstatsPTMFormat > ### Title: Import Metamorpheus files into PTM format > ### Aliases: MetamorpheusToMSstatsPTMFormat > > ### ** Examples > > input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", + package = "MSstatsPTM") > input = data.table::fread(input) > annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", + package = "MSstatsPTM") > annot = data.table::fread(annot) > input_protein = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv", + package = "MSstatsPTM") > input_protein = data.table::fread(input_protein) > annot_protein = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv", + package = "MSstatsPTM") > annot_protein = data.table::fread(annot_protein) > fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", + package="MSstatsPTM") > metamorpheus_imported = MetamorpheusToMSstatsPTMFormat( + input, + annot, + fasta_path=fasta_path, + input_protein=input_protein, + annotation_protein=annot_protein, + use_unmod_peptides=FALSE, + mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]") + ) [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, : Assertion on 'append' failed: Must be of type 'logical', not 'NULL'. Calls: MetamorpheusToMSstatsPTMFormat ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ Running ‘tinytest.R’ ERROR Running the tests in ‘tests/tinytest.R’ failed. Last 13 lines of output: 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;31m1 fails[0m test_converters.R............. 52 tests [0;31m2 fails[0m test_converters.R............. 53 tests [0;31m3 fails[0m test_converters.R............. 54 tests [0;31m3 fails[0m test_converters.R............. 55 tests [0;31m3 fails[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, : Assertion on 'append' failed: Must be of type 'logical', not 'NULL'. Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted * 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: 2 ERRORs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-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/4.5-x86_64/Resources/library’ * installing *source* package ‘MSstatsPTM’ ... ** this is package ‘MSstatsPTM’ version ‘2.10.1’ ** 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/4.5-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/4.5-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 installing to /Library/Frameworks/R.framework/Versions/4.5-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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 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 12.760 0.836 13.870
MSstatsPTM.Rcheck/tests/tinytest.Rout.fail
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 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 [2025-08-01 06:57:00] ** Raw data from MaxQuant imported successfully. INFO [2025-08-01 06:57:00] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2025-08-01 06:57:00] ** Rows with values of Reverse equal to + are removed INFO [2025-08-01 06:57:00] ** Features with all missing measurements across channels within each run are removed. INFO [2025-08-01 06:57:00] ** Using provided annotation. INFO [2025-08-01 06:57:00] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:00] ** 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 kept. INFO [2025-08-01 06:57:00] ** Features with all missing measurements across channels within each run are removed. INFO [2025-08-01 06:57:00] ** Shared peptides are removed. INFO [2025-08-01 06:57:00] ** Features with all missing measurements across channels within each run are removed. INFO [2025-08-01 06:57:00] ** PSMs have been aggregated to peptide ions. INFO [2025-08-01 06:57:00] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:00] ** Features with one or two measurements across channels within each run are removed. INFO [2025-08-01 06:57:00] ** Fractionation handled. INFO [2025-08-01 06:57:00] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:00] ** 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 [2025-08-01 06:57:01] ** Raw data from MaxQuant imported successfully. INFO [2025-08-01 06:57:01] ** Rows with values of Potentialcontaminant equal to + are removed INFO [2025-08-01 06:57:01] ** Rows with values of Reverse equal to + are removed INFO [2025-08-01 06:57:01] ** Using provided annotation. INFO [2025-08-01 06:57:01] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:01] ** 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 [2025-08-01 06:57:01] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:01] ** Shared peptides are removed. INFO [2025-08-01 06:57:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:01] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:01] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:01] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:01] ** Fractionation handled. INFO [2025-08-01 06:57:01] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:01] ** 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 [2025-08-01 06:57:07] ** Raw data from Spectronaut imported successfully. INFO [2025-08-01 06:57:07] ** Raw data from Spectronaut cleaned successfully. INFO [2025-08-01 06:57:07] ** Using provided annotation. INFO [2025-08-01 06:57:07] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:07] ** 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 [2025-08-01 06:57:07] ** PGQvalue not found in input columns. WARN [2025-08-01 06:57:07] ** EGQvalue not found in input columns. INFO [2025-08-01 06:57:07] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:07] ** Shared peptides are removed. INFO [2025-08-01 06:57:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:07] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:07] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:07] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:07] ** Fractionation handled. INFO [2025-08-01 06:57:07] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:07] ** 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 [2025-08-01 06:57:09] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:09] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:09] ** Using provided annotation. INFO [2025-08-01 06:57:09] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:09] ** 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 [2025-08-01 06:57:09] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:09] ** Shared peptides are removed. INFO [2025-08-01 06:57:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:09] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:09] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:09] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:09] ** Fractionation handled. INFO [2025-08-01 06:57:09] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:09] ** 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 [2025-08-01 06:57:11] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:11] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:11] ** Using provided annotation. INFO [2025-08-01 06:57:11] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:11] ** 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 [2025-08-01 06:57:11] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:11] ** Shared peptides are removed. INFO [2025-08-01 06:57:11] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:12] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:12] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:12] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:12] ** Fractionation handled. INFO [2025-08-01 06:57:12] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:12] ** 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 [2025-08-01 06:57:14] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:14] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:14] ** Using provided annotation. INFO [2025-08-01 06:57:14] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:14] ** 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 [2025-08-01 06:57:14] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:14] ** Shared peptides are removed. INFO [2025-08-01 06:57:14] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:14] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:14] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:14] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:14] ** Fractionation handled. INFO [2025-08-01 06:57:14] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:14] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 38 tests [0;32mOK[0m INFO [2025-08-01 06:57:16] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:16] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:16] ** Using provided annotation. INFO [2025-08-01 06:57:16] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:16] ** 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 [2025-08-01 06:57:16] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:16] ** Shared peptides are removed. INFO [2025-08-01 06:57:16] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:16] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:16] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:16] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:16] ** Fractionation handled. INFO [2025-08-01 06:57:16] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:16] ** 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 [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:19] ** Using provided annotation. INFO [2025-08-01 06:57:19] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:19] ** 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 [2025-08-01 06:57:19] ** Features with all missing measurements across runs are removed. INFO [2025-08-01 06:57:19] ** Shared peptides are removed. INFO [2025-08-01 06:57:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2025-08-01 06:57:19] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:19] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:19] ** Features with one or two measurements across runs are removed. INFO [2025-08-01 06:57:19] ** Fractionation handled. INFO [2025-08-01 06:57:19] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:19] ** 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 [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:19] ** Using provided annotation. INFO [2025-08-01 06:57:19] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:19] ** 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 [2025-08-01 06:57:19] ** Features with all missing measurements across channels within each run are removed. INFO [2025-08-01 06:57:19] ** Shared peptides are removed. INFO [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed. INFO [2025-08-01 06:57:19] ** PSMs have been aggregated to peptide ions. INFO [2025-08-01 06:57:19] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed. INFO [2025-08-01 06:57:19] ** Fractionation handled. INFO [2025-08-01 06:57:19] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:19] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function. INFO [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-08-01 06:57:19] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-08-01 06:57:19] ** Using provided annotation. INFO [2025-08-01 06:57:19] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2025-08-01 06:57:19] ** 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 [2025-08-01 06:57:19] ** Features with all missing measurements across channels within each run are removed. INFO [2025-08-01 06:57:19] ** Shared peptides are removed. INFO [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed. INFO [2025-08-01 06:57:19] ** PSMs have been aggregated to peptide ions. INFO [2025-08-01 06:57:19] ** Run annotation merged with quantification data. INFO [2025-08-01 06:57:19] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance. INFO [2025-08-01 06:57:19] ** Fractions belonging to same mixture have been combined. INFO [2025-08-01 06:57:19] ** Features with one or two measurements across channels within each run are removed. INFO [2025-08-01 06:57:19] ** Fractionation handled. INFO [2025-08-01 06:57:19] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2025-08-01 06:57:19] ** 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;31m1 fails[0m test_converters.R............. 52 tests [0;31m2 fails[0m test_converters.R............. 53 tests [0;31m3 fails[0m test_converters.R............. 54 tests [0;31m3 fails[0m test_converters.R............. 55 tests [0;31m3 fails[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, : Assertion on 'append' failed: Must be of type 'logical', not 'NULL'. Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> makeAssertion -> mstop In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
name | user | system | elapsed | |
DIANNtoMSstatsPTMFormat | 0.000 | 0.001 | 0.001 | |
FragPipetoMSstatsPTMFormat | 1.845 | 0.063 | 2.051 | |
MSstatsPTMSiteLocator | 0 | 0 | 0 | |
MaxQtoMSstatsPTMFormat | 0.863 | 0.073 | 0.990 | |