Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -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 1353/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstatsLiP 1.12.0 (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 MSstatsLiP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsLiP.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: MSstatsLiP |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstatsLiP_1.12.0.tar.gz |
StartedAt: 2024-12-20 03:17:23 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 03:24:26 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 422.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MSstatsLiP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstatsLiP_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsLiP.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MSstatsLiP’ version ‘1.12.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MSstatsLiP’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ResistanceBarcodePlotLiP: no visible binding for global variable ‘GROUP’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Protein’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘uniprot_iso’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘PeptideSequence’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Accessibility_ratio’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Index’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Label’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘sig’ ResistanceBarcodePlotLiP: no visible binding for global variable ‘Coverage’ StructuralBarcodePlotLiP: no visible binding for global variable ‘NSEMI_TRI’ StructuralBarcodePlotLiP: no visible binding for global variable ‘CSEMI_TRI’ calculateProteolyticResistance: no visible binding for global variable ‘LogIntensities’ calculateProteolyticResistance: no visible binding for global variable ‘Protein.y’ Undefined global functions or variables: Accessibility_ratio CSEMI_TRI Coverage GROUP Index Label LogIntensities NSEMI_TRI PeptideSequence Protein Protein.y sig uniprot_iso * 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 ... OK * 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 dataProcessPlotsLiP 18.678 0.212 18.892 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsLiP.Rcheck/00check.log’ for details.
MSstatsLiP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MSstatsLiP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MSstatsLiP’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o MSstatsLiP.so RcppExports.o model_adjustment.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-MSstatsLiP/00new/MSstatsLiP/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 (MSstatsLiP)
MSstatsLiP.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-pc-linux-gnu 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("MSstatsLiP") + } test_SkylinetoMSstatsLiPFormat.R 0 tests FUNCTION DEPRECATION NOTICE: We would like to notify you that the SkylinetoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SkylinetoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SkylinetoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. FUNCTION DEPRECATION NOTICE: We would like to notify you that the SkylinetoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SkylinetoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SkylinetoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. test_SkylinetoMSstatsLiPFormat.R 1 tests [0;32mOK[0m FUNCTION DEPRECATION NOTICE: We would like to notify you that the SkylinetoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SkylinetoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SkylinetoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. test_SkylinetoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. test_SkylinetoMSstatsLiPFormat.R 3 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 4 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 5 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 6 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 7 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 8 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 9 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Skyline imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Skyline cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. test_SkylinetoMSstatsLiPFormat.R 10 tests [0;32mOK[0m [0;34m0.3s[0m test_SpectronauttoMSstatsLiPFormat.R 0 tests test_SpectronauttoMSstatsLiPFormat.R 0 tests FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. test_SpectronauttoMSstatsLiPFormat.R 1 tests [0;32mOK[0m FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. test_SpectronauttoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2024-12-20 03:23:21] ** Raw data from Spectronaut imported successfully. INFO [2024-12-20 03:23:21] ** Raw data from Spectronaut cleaned successfully. INFO [2024-12-20 03:23:21] ** Using annotation extracted from quantification data. INFO [2024-12-20 03:23:21] ** Run labels were standardized to remove symbols such as '.' or '%'. INFO [2024-12-20 03:23:21] ** 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 03:23:21] ** PGQvalue not found in input columns. INFO [2024-12-20 03:23:21] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0 INFO [2024-12-20 03:23:21] ** Features with all missing measurements across runs are removed. INFO [2024-12-20 03:23:21] ** Shared peptides are removed. INFO [2024-12-20 03:23:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max INFO [2024-12-20 03:23:21] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 03:23:21] ** Run annotation merged with quantification data. INFO [2024-12-20 03:23:21] ** Features with one or two measurements across runs are removed. INFO [2024-12-20 03:23:21] ** Fractionation handled. INFO [2024-12-20 03:23:21] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-20 03:23:22] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function. FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow. test_SpectronauttoMSstatsLiPFormat.R 3 tests [0;32mOK[0m test_SpectronauttoMSstatsLiPFormat.R 4 tests [0;32mOK[0m test_SpectronauttoMSstatsLiPFormat.R 5 tests [0;32mOK[0m test_SpectronauttoMSstatsLiPFormat.R 6 tests [0;32mOK[0m INFO [2024-12-20 03:23:22] ** Raw data from Spectronaut imported successfully. INFO [2024-12-20 03:23:22] ** Raw data from Spectronaut cleaned successfully. INFO [2024-12-20 03:23:22] ** Using annotation extracted from quantification data. INFO [2024-12-20 03:23:22] ** Run labels were standardized to remove symbols such as '.' or '%'. test_SpectronauttoMSstatsLiPFormat.R 7 tests [0;32mOK[0m test_SpectronauttoMSstatsLiPFormat.R 8 tests [0;32mOK[0m test_SpectronauttoMSstatsLiPFormat.R 9 tests [0;32mOK[0m [0;34m0.8s[0m test_dataProcessPlotsLiP.R.... 0 tests test_dataProcessPlotsLiP.R.... 1 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 2 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 3 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 4 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 5 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 6 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 7 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 8 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 9 tests [0;32mOK[0m test_dataProcessPlotsLiP.R.... 10 tests [0;32mOK[0m Drew the Profile plot for P14164_ILQNDLK (1 of 14) Drew the Profile plot for P17891_ALQLINQDDADIIGGRDR (2 of 14) Drew the Profile plot for P17891_DDDTDFLK (3 of 14) Drew the Profile plot for P36112_SNDLLSGLTGSSQTR (4 of 14) Drew the Profile plot for P38805_LGQTVGR (5 of 14) Drew the Profile plot for P46959_DIIGKPYGSQIAIR (6 of 14) Drew the Profile plot for P52893_SSSQGVEGIRK (7 of 14) Drew the Profile plot for P52911_TWITEDDFEQIK (8 of 14) Drew the Profile plot for P53235_ERQAVGDKLEDTQVLK (9 of 14) Drew the Profile plot for P53858_FLDNHEVDSIVSLER (10 of 14) Drew the Profile plot for Q02908_ISVISGVGVR (11 of 14) Drew the Profile plot for Q12248_EFQSVSDLWK (12 of 14) Drew the Profile plot for P16622_SHLQSNQLYSNQLPLDFALGK (13 of 14) Drew the Profile plot for P24004_FIGASEQNIR (14 of 14) Drew the Profile plot for P14164_ILQNDLK ( 1 of 14 ) Drew the Profile plot for P17891_ALQLINQDDADIIGGRDR ( 2 of 14 ) Drew the Profile plot for P17891_DDDTDFLK ( 3 of 14 ) Drew the Profile plot for P36112_SNDLLSGLTGSSQTR ( 4 of 14 ) Drew the Profile plot for P38805_LGQTVGR ( 5 of 14 ) Drew the Profile plot for P46959_DIIGKPYGSQIAIR ( 6 of 14 ) Drew the Profile plot for P52893_SSSQGVEGIRK ( 7 of 14 ) Drew the Profile plot for P52911_TWITEDDFEQIK ( 8 of 14 ) Drew the Profile plot for P53235_ERQAVGDKLEDTQVLK ( 9 of 14 ) Drew the Profile plot for P53858_FLDNHEVDSIVSLER ( 10 of 14 ) Drew the Profile plot for Q02908_ISVISGVGVR ( 11 of 14 ) Drew the Profile plot for Q12248_EFQSVSDLWK ( 12 of 14 ) Drew the Profile plot for P16622_SHLQSNQLYSNQLPLDFALGK ( 13 of 14 ) Drew the Profile plot for P24004_FIGASEQNIR ( 14 of 14 ) test_dataProcessPlotsLiP.R.... 11 tests [0;32mOK[0m Drew the Quality Contol plot(boxplot) for all ptms/proteins. Drew the Quality Contol plot(boxplot) for P14164_ILQNDLK (1 of 14) Drew the Quality Contol plot(boxplot) for P17891_ALQLINQDDADIIGGRDR (2 of 14) Drew the Quality Contol plot(boxplot) for P17891_DDDTDFLK (3 of 14) Drew the Quality Contol plot(boxplot) for P36112_SNDLLSGLTGSSQTR (4 of 14) Drew the Quality Contol plot(boxplot) for P38805_LGQTVGR (5 of 14) Drew the Quality Contol plot(boxplot) for P46959_DIIGKPYGSQIAIR (6 of 14) Drew the Quality Contol plot(boxplot) for P52893_SSSQGVEGIRK (7 of 14) Drew the Quality Contol plot(boxplot) for P52911_TWITEDDFEQIK (8 of 14) Drew the Quality Contol plot(boxplot) for P53235_ERQAVGDKLEDTQVLK (9 of 14) Drew the Quality Contol plot(boxplot) for P53858_FLDNHEVDSIVSLER (10 of 14) Drew the Quality Contol plot(boxplot) for Q02908_ISVISGVGVR (11 of 14) Drew the Quality Contol plot(boxplot) for Q12248_EFQSVSDLWK (12 of 14) Drew the Quality Contol plot(boxplot) for P16622_SHLQSNQLYSNQLPLDFALGK (13 of 14) Drew the Quality Contol plot(boxplot) for P24004_FIGASEQNIR (14 of 14) test_dataProcessPlotsLiP.R.... 12 tests [0;32mOK[0m [0;34m19.4s[0m test_dataSummarizationLiP.R... 0 tests test_dataSummarizationLiP.R... 0 tests test_dataSummarizationLiP.R... 1 tests [0;32mOK[0m test_dataSummarizationLiP.R... 2 tests [0;32mOK[0m test_dataSummarizationLiP.R... 3 tests [0;32mOK[0m test_dataSummarizationLiP.R... 4 tests [0;32mOK[0m test_dataSummarizationLiP.R... 5 tests [0;32mOK[0m test_dataSummarizationLiP.R... 6 tests [0;32mOK[0m test_dataSummarizationLiP.R... 7 tests [0;32mOK[0m test_dataSummarizationLiP.R... 8 tests [0;32mOK[0m test_dataSummarizationLiP.R... 9 tests [0;32mOK[0m test_dataSummarizationLiP.R... 10 tests [0;32mOK[0m test_dataSummarizationLiP.R... 11 tests [0;32mOK[0m test_dataSummarizationLiP.R... 12 tests [0;32mOK[0m test_dataSummarizationLiP.R... 13 tests [0;32mOK[0m test_dataSummarizationLiP.R... 14 tests [0;32mOK[0m test_dataSummarizationLiP.R... 15 tests [0;32mOK[0m test_dataSummarizationLiP.R... 16 tests [0;32mOK[0m test_dataSummarizationLiP.R... 17 tests [0;32mOK[0m test_dataSummarizationLiP.R... 18 tests [0;32mOK[0m test_dataSummarizationLiP.R... 19 tests [0;32mOK[0m test_dataSummarizationLiP.R... 20 tests [0;32mOK[0m test_dataSummarizationLiP.R... 21 tests [0;32mOK[0m test_dataSummarizationLiP.R... 22 tests [0;32mOK[0m test_dataSummarizationLiP.R... 23 tests [0;32mOK[0m test_dataSummarizationLiP.R... 24 tests [0;32mOK[0m test_dataSummarizationLiP.R... 25 tests [0;32mOK[0m test_dataSummarizationLiP.R... 26 tests [0;32mOK[0m test_dataSummarizationLiP.R... 27 tests [0;32mOK[0m test_dataSummarizationLiP.R... 28 tests [0;32mOK[0m Starting PTM summarization... test_dataSummarizationLiP.R... 29 tests [0;32mOK[0m [0;34m0.1s[0m test_groupComparisonLiP.R..... 0 tests test_groupComparisonLiP.R..... 0 tests test_groupComparisonLiP.R..... 1 tests [0;32mOK[0m test_groupComparisonLiP.R..... 2 tests [0;32mOK[0m Starting PTM modeling... test_groupComparisonLiP.R..... 3 tests [0;32mOK[0m Starting PTM modeling... INFO [2024-12-20 03:23:42] == Start to test and get inference in whole plot ... | | | 0% | |===== | 7% | |========== | 14% | |=============== | 21% | |==================== | 29% | |========================= | 36% | |============================== | 43% | |=================================== | 50% | |======================================== | 57% | |============================================= | 64% | |================================================== | 71% | |======================================================= | 79% | |============================================================ | 86% | |================================================================= | 93% | |======================================================================| 100% INFO [2024-12-20 03:23:42] == Comparisons for all proteins are done. Starting Protein modeling... INFO [2024-12-20 03:23:42] == Start to test and get inference in whole plot ... | | | 0% | |===== | 8% | |=========== | 15% | |================ | 23% | |====================== | 31% | |=========================== | 38% | |================================ | 46% | |====================================== | 54% | |=========================================== | 62% | |================================================ | 69% | |====================================================== | 77% | |=========================================================== | 85% | |================================================================= | 92% | |======================================================================| 100% INFO [2024-12-20 03:23:42] == Comparisons for all proteins are done. Starting adjustment... test_groupComparisonLiP.R..... 3 tests [0;32mOK[0m test_groupComparisonLiP.R..... 4 tests [0;32mOK[0m test_groupComparisonLiP.R..... 5 tests [0;32mOK[0m test_groupComparisonLiP.R..... 6 tests [0;32mOK[0m test_groupComparisonLiP.R..... 7 tests [0;32mOK[0m test_groupComparisonLiP.R..... 8 tests [0;32mOK[0m test_groupComparisonLiP.R..... 9 tests [0;32mOK[0m test_groupComparisonLiP.R..... 10 tests [0;32mOK[0m [0;34m0.5s[0m test_groupComparisonPlotsLiP.R 0 tests test_groupComparisonPlotsLiP.R 1 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 2 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 3 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 4 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 5 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 6 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 7 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 8 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 9 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 10 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 11 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 12 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 13 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 14 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 15 tests [0;32mOK[0m test_groupComparisonPlotsLiP.R 16 tests [0;32mOK[0m [0;34m3.6s[0m test_trypticHistogramLiP.R.... 0 tests test_trypticHistogramLiP.R.... 0 tests test_trypticHistogramLiP.R.... 0 tests test_trypticHistogramLiP.R.... 1 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 2 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 3 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 4 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 5 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 6 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 7 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 8 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 9 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 10 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 11 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 12 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 13 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 14 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 15 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 16 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 17 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 18 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 19 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 20 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 21 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 22 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 23 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 24 tests [0;32mOK[0m test_trypticHistogramLiP.R.... 25 tests [0;32mOK[0m [0;34m7.5s[0m All ok, 111 results (32.1s) Warning message: In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) : no non-missing arguments to max; returning -Inf > > proc.time() user system elapsed 36.892 1.009 37.713
MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings
name | user | system | elapsed | |
DIANNtoMSstatsLiPFormat | 0.012 | 0.007 | 0.019 | |
LiPRawData | 0.008 | 0.002 | 0.008 | |
MSstatsLiP_Summarized | 0.012 | 0.003 | 0.015 | |
MSstatsLiP_data | 0.021 | 0.001 | 0.023 | |
MSstatsLiP_model | 0.010 | 0.000 | 0.011 | |
PCAPlotLiP | 1.422 | 0.084 | 1.507 | |
ResistanceBarcodePlotLiP | 0.001 | 0.000 | 0.001 | |
SkylineTest | 0.004 | 0.000 | 0.006 | |
SkylinetoMSstatsLiPFormat | 0.004 | 0.000 | 0.005 | |
SpectronauttoMSstatsLiPFormat | 0.645 | 0.036 | 0.642 | |
StructuralBarcodePlotLiP | 2.927 | 0.068 | 2.996 | |
TrPRawData | 0.004 | 0.001 | 0.006 | |
annotSite | 0.001 | 0.000 | 0.000 | |
calculateProteolyticResistance | 0.006 | 0.000 | 0.006 | |
calculateTrypticity | 0.012 | 0.000 | 0.012 | |
correlationPlotLiP | 0.222 | 0.002 | 0.224 | |
dataProcessPlotsLiP | 18.678 | 0.212 | 18.892 | |
dataSummarizationLiP | 0.572 | 0.003 | 0.515 | |
groupComparisonLiP | 0.761 | 0.040 | 0.800 | |
groupComparisonPlotsLiP | 1.246 | 0.001 | 1.247 | |
locateMod | 0 | 0 | 0 | |
locatePTM | 0.052 | 0.000 | 0.052 | |
raw_lip | 0.040 | 0.003 | 0.043 | |
raw_prot | 0.044 | 0.002 | 0.046 | |
tidyFasta | 0.020 | 0.000 | 0.019 | |
trypticHistogramLiP | 0.250 | 0.003 | 0.240 | |