Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1338/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstatsPTM 2.7.0 (landing page) Devon Kohler
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 2.7.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSstatsPTM_2.7.0.tar.gz |
StartedAt: 2024-08-21 03:04:46 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:09:15 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 268.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MSstatsPTM.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MSstatsPTM_2.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MSstatsPTM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MSstatsPTM' version '2.7.0' * 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 whether package 'MSstatsPTM' can be installed ... WARNING Found the following significant warnings: Warning: MSstatsPTM.Rd:3: docType '_PACKAGE' is unrecognized See 'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck/00install.out' for details. * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... WARNING prepare_Rd: MSstatsPTM.Rd:3: docType '_PACKAGE' is unrecognized * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/MSstatsPTM/libs/x64/MSstatsPTM.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed groupComparisonPlotsPTM 14.95 0.22 15.17 dataSummarizationPTM_TMT 5.81 0.30 6.19 designSampleSizePTM 5.81 0.12 6.00 groupComparisonPTM 4.89 0.13 5.05 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck/00check.log' for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MSstatsPTM' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++17 -shared -s -static-libgcc -o MSstatsPTM.dll tmp.def RcppExports.o model_adjustment.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Warning: MSstatsPTM.Rd:3: docType '_PACKAGE' is unrecognized *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsPTM)
MSstatsPTM.Rcheck/tests/tinytest.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > if ( requireNamespace("tinytest", quietly=TRUE) ){ + 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 test_converters.R............. 5 tests [0;32mOK[0m test_converters.R............. 5 tests [0;32mOK[0m test_converters.R............. 6 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............. 10 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............. 13 tests [0;32mOK[0m test_converters.R............. 14 tests [0;32mOK[0m test_converters.R............. 14 tests [0;32mOK[0m test_converters.R............. 14 tests [0;32mOK[0m test_converters.R............. 14 tests [0;32mOK[0m INFO [2024-08-21 03:08:31] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-08-21 03:08:31] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-08-21 03:08:31] ** Using provided annotation. INFO [2024-08-21 03:08:31] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:31] ** 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 [2024-08-21 03:08:31] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:31] ** Shared peptides are removed. INFO [2024-08-21 03:08:31] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:31] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:31] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:31] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:31] ** Fractionation handled. INFO [2024-08-21 03:08:31] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:31] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 15 tests [0;32mOK[0m INFO: Extracting modifications INFO [2024-08-21 03:08:32] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-08-21 03:08:32] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-08-21 03:08:32] ** Using provided annotation. INFO [2024-08-21 03:08:32] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:32] ** 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 [2024-08-21 03:08:32] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:32] ** Shared peptides are removed. INFO [2024-08-21 03:08:33] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:33] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:33] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:33] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:33] ** Fractionation handled. INFO [2024-08-21 03:08:33] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:33] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 16 tests [0;32mOK[0m INFO: Extracting modifications INFO [2024-08-21 03:08:34] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-08-21 03:08:34] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-08-21 03:08:34] ** Using provided annotation. INFO [2024-08-21 03:08:34] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:34] ** 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 [2024-08-21 03:08:34] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:34] ** Shared peptides are removed. INFO [2024-08-21 03:08:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:34] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:34] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:34] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:34] ** Fractionation handled. INFO [2024-08-21 03:08:34] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 17 tests [0;32mOK[0m INFO [2024-08-21 03:08:35] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-08-21 03:08:35] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-08-21 03:08:35] ** Using provided annotation. INFO [2024-08-21 03:08:35] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:35] ** 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 across runs will be removed. INFO [2024-08-21 03:08:35] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:35] ** Shared peptides are removed. INFO [2024-08-21 03:08:35] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:35] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:35] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:35] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:35] ** Fractionation handled. INFO [2024-08-21 03:08:35] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:35] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 18 tests [0;32mOK[0m test_converters.R............. 19 tests [0;32mOK[0m INFO [2024-08-21 03:08:36] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2024-08-21 03:08:36] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2024-08-21 03:08:36] ** Using provided annotation. INFO [2024-08-21 03:08:36] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:36] ** 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 [2024-08-21 03:08:36] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:36] ** Shared peptides are removed. INFO [2024-08-21 03:08:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:36] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:36] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:36] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:36] ** Fractionation handled. INFO [2024-08-21 03:08:36] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. 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............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m test_converters.R............. 22 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus imported successfully. INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-08-21 03:08:37] ** Using provided annotation. INFO [2024-08-21 03:08:37] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:37] ** 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 [2024-08-21 03:08:37] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Shared peptides are removed. INFO [2024-08-21 03:08:37] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Fractionation handled. INFO [2024-08-21 03:08:37] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:37] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus imported successfully. INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-08-21 03:08:37] ** Using provided annotation. INFO [2024-08-21 03:08:37] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:37] ** 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 [2024-08-21 03:08:37] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Shared peptides are removed. INFO [2024-08-21 03:08:37] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Fractionation handled. INFO [2024-08-21 03:08:37] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:37] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 22 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 test_converters.R............. 29 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications." INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus imported successfully. INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-08-21 03:08:37] ** Using provided annotation. INFO [2024-08-21 03:08:37] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:37] ** 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 [2024-08-21 03:08:37] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Shared peptides are removed. INFO [2024-08-21 03:08:37] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Fractionation handled. INFO [2024-08-21 03:08:37] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:37] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus imported successfully. INFO [2024-08-21 03:08:37] ** Raw data from Metamorpheus cleaned successfully. INFO [2024-08-21 03:08:37] ** Using provided annotation. INFO [2024-08-21 03:08:37] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-08-21 03:08:37] ** 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 [2024-08-21 03:08:37] ** Features with all missing measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Shared peptides are removed. INFO [2024-08-21 03:08:37] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Run annotation merged with quantification data. INFO [2024-08-21 03:08:37] ** Features with one or two measurements across runs are removed. INFO [2024-08-21 03:08:37] ** Fractionation handled. INFO [2024-08-21 03:08:37] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-08-21 03:08:37] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. test_converters.R............. 29 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............. 36 tests [0;32mOK[0m [0;34m11.1s[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;34m0.3s[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;34m0.3s[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... 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|======================================================================| 100% INFO [2024-08-21 03:08:46] == Comparisons for all proteins are done. Starting Protein modeling... 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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 [2024-08-21 03:08:48] Design: 2 mixtures. INFO [2024-08-21 03:08:48] Design: 1 MS run per mixture. INFO [2024-08-21 03:08:48] Design: group comparison design (Different conditions contains different biological subjects). 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|======================================================================| 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;34m20.9s[0m All ok, 115 results (32.6s) There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 37.42 1.89 39.39
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
name | user | system | elapsed | |
DIANNtoMSstatsPTMFormat | 0 | 0 | 0 | |
FragPipetoMSstatsPTMFormat | 0.51 | 0.06 | 0.59 | |
MSstatsPTMSiteLocator | 0 | 0 | 0 | |
MaxQtoMSstatsPTMFormat | 0.94 | 0.07 | 1.01 | |
MetamorpheusToMSstatsPTMFormat | 0.16 | 0.04 | 0.22 | |
PDtoMSstatsPTMFormat | 1.09 | 0.12 | 1.25 | |
PStoMSstatsPTMFormat | 0.11 | 0.00 | 0.10 | |
ProgenesistoMSstatsPTMFormat | 0.06 | 0.00 | 0.07 | |
SkylinetoMSstatsPTMFormat | 0.07 | 0.02 | 0.08 | |
SpectronauttoMSstatsPTMFormat | 0.62 | 0.02 | 0.65 | |
annotSite | 0 | 0 | 0 | |
dataProcessPlotsPTM | 2.55 | 0.03 | 2.61 | |
dataSummarizationPTM | 2.69 | 0.09 | 2.78 | |
dataSummarizationPTM_TMT | 5.81 | 0.30 | 6.19 | |
designSampleSizePTM | 5.81 | 0.12 | 6.00 | |
fragpipe_annotation | 0 | 0 | 0 | |
fragpipe_annotation_protein | 0 | 0 | 0 | |
fragpipe_input | 0.02 | 0.00 | 0.02 | |
fragpipe_input_protein | 0 | 0 | 0 | |
groupComparisonPTM | 4.89 | 0.13 | 5.05 | |
groupComparisonPlotsPTM | 14.95 | 0.22 | 15.17 | |
locateMod | 0 | 0 | 0 | |
locatePTM | 0.02 | 0.01 | 0.03 | |
maxq_lf_annotation | 0 | 0 | 0 | |
maxq_lf_evidence | 0.01 | 0.00 | 0.02 | |
maxq_tmt_annotation | 0 | 0 | 0 | |
maxq_tmt_evidence | 0.01 | 0.00 | 0.02 | |
pd_annotation | 0 | 0 | 0 | |
pd_psm_input | 0.02 | 0.00 | 0.02 | |
pd_testing_output | 0.33 | 0.12 | 0.45 | |
raw.input | 0.07 | 0.00 | 0.08 | |
raw.input.tmt | 0.02 | 0.00 | 0.02 | |
spectronaut_annotation | 0 | 0 | 0 | |
spectronaut_input | 0 | 0 | 0 | |
summary.data | 0.58 | 0.19 | 0.77 | |
summary.data.tmt | 1.00 | 0.39 | 1.39 | |
tidyFasta | 0.01 | 0.00 | 0.01 | |