Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1344/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MSstats 4.15.0 (landing page) Meena Choi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MSstats package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstats.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: MSstats |
Version: 4.15.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstats.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MSstats_4.15.0.tar.gz |
StartedAt: 2024-12-24 02:57:51 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 03:00:38 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 167.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MSstats.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstats.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MSstats_4.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MSstats.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MSstats/DESCRIPTION' ... OK * this is package 'MSstats' version '4.15.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'MSstats' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'statmod' All declared Imports should be used. Unexported object imported by a ':::' call: '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 .plotHeatmap : <anonymous>: no visible global function definition for 'col2rgb' .plotProfile: no visible binding for global variable 'newABUNDANCE' .savePlotlyPlotHTML: no visible global function definition for 'zip' .setCensoredByThreshold: no visible binding for global variable 'any_censored' DIANNtoMSstatsFormat: no visible binding for global variable 'DetectionQValue' DIANNtoMSstatsFormat: no visible binding for global variable 'LibPGQValue' DIANNtoMSstatsFormat: no visible binding for global variable 'LibQValue' DIANNtoMSstatsFormat: no visible binding for global variable 'GlobalPGQValue' DIANNtoMSstatsFormat: no visible binding for global variable 'GlobalQValue' MSstatsPrepareForSummarization: no visible binding for global variable 'ref' MSstatsPrepareForSummarization: no visible binding for global variable 'LABEL' MSstatsPrepareForSummarization: no visible binding for global variable 'RUN' SDRFtoAnnotation: no visible binding for global variable '..extract_cols' extractSDRF: no visible binding for global variable '..extract_cols' validateAnnotation: no visible binding for global variable 'BioReplicate' validateAnnotation: no visible binding for global variable 'Condition' Undefined global functions or variables: ..extract_cols BioReplicate Condition DetectionQValue GlobalPGQValue GlobalQValue LABEL LibPGQValue LibQValue RUN any_censored col2rgb newABUNDANCE ref zip Consider adding importFrom("grDevices", "col2rgb") importFrom("utils", "zip") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) MSstatsSummarizationOutput.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MSstatsSummarizationOutput.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) MSstatsSummarizationOutput.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... WARNING Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd': 'removeFewMeasurements' 'useUniquePeptide' 'summaryforMultipleRows' 'removeProtein_with1Feature' 'removeProtein_with1Peptide' 'removeOxidationMpeptides' 'removeMpeptides' 'use_log_file' 'append' 'verbose' 'log_file_path' Documented arguments not in \usage in Rd file 'dot-getContrast.Rd': 'contrast_matrix' Documented arguments not in \usage in Rd file 'dot-getSingleProteinForProfile.Rd': 'dataProcess' Documented arguments not in \usage in Rd file 'dot-getWideTable.Rd': 'vector' Undocumented arguments in Rd file 'modelBasedQCPlots.Rd' 'displayDeprecationMessage' 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/MSstats/libs/x64/MSstats.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 dataProcessPlots 7.07 0.12 7.20 dot-makeQCPlot 6.06 0.08 6.14 * 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: 1 WARNING, 5 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/MSstats.Rcheck/00check.log' for details.
MSstats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MSstats ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'MSstats' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++11 g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c comparison_contrasts.cpp -o comparison_contrasts.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linear_summary.cpp -o linear_summary.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c median_polish.cpp -o median_polish.o g++ -shared -s -static-libgcc -o MSstats.dll tmp.def RcppExports.o common.o comparison_contrasts.o linear_summary.o median_polish.o -fopenmp -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRlapack -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-MSstats/00new/MSstats/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstats)
MSstats.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if ( requireNamespace("tinytest", quietly=TRUE) ){ + tinytest::test_package("MSstats") + } Attaching package: 'MSstats' The following object is masked from 'package:grDevices': savePlot test_MSstatsdev.R............. 1 tests [0;32mOK[0m [0;36m57ms[0m INFO [2024-12-24 03:00:10] ** Features with one or two measurements across runs are removed. INFO [2024-12-24 03:00:10] ** Fractionation handled. INFO [2024-12-24 03:00:10] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-24 03:00:10] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-12-24 03:00:10] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-12-24 03:00:10] ** Use all features that the dataset originally has. INFO [2024-12-24 03:00:10] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-12-24 03:00:10] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-12-24 03:00:10] == Start the summarization per subplot... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-12-24 03:00:10] == Summarization is done. test_dataProcess.R............ 0 tests INFO [2024-12-24 03:00:10] ** Features with one or two measurements across runs are removed. INFO [2024-12-24 03:00:10] ** Fractionation handled. INFO [2024-12-24 03:00:10] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-24 03:00:10] ** Use all features that the dataset originally has. INFO [2024-12-24 03:00:10] # proteins: 6 # peptides per protein: 11-32 # features per peptide: 1-1 INFO [2024-12-24 03:00:10] C1 C2 C3 C4 C5 C6 # runs 3 3 3 3 3 3 # bioreplicates 1 1 1 1 1 1 # tech. replicates 3 3 3 3 3 3 INFO [2024-12-24 03:00:10] Some features are completely missing in at least one condition: D.GPLTGTYR_23_23_NA_NA, F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA, G.PLTGTYR_8_8_NA_NA, H.SFNVEYDDSQDK_465_465_NA_NA, K.AVVQDPALKPL_156_156_NA_NA ... INFO [2024-12-24 03:00:10] == Start the summarization per subplot... | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% INFO [2024-12-24 03:00:10] == Summarization is done. test_dataProcess.R............ 0 tests INFO [2024-12-24 03:00:10] ** Features with one or two measurements across runs are removed. INFO [2024-12-24 03:00:10] ** Fractionation handled. INFO [2024-12-24 03:00:10] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-24 03:00:10] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-12-24 03:00:10] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-12-24 03:00:10] ** Use all features that the dataset originally has. INFO [2024-12-24 03:00:10] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-12-24 03:00:10] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-12-24 03:00:10] == Start the summarization per subplot... INFO [2024-12-24 03:00:14] == Summarization is done. test_dataProcess.R............ 0 tests INFO [2024-12-24 03:00:14] ** Features with one or two measurements across runs are removed. INFO [2024-12-24 03:00:14] ** Fractionation handled. INFO [2024-12-24 03:00:14] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-24 03:00:14] ** Use all features that the dataset originally has. INFO [2024-12-24 03:00:14] # proteins: 6 # peptides per protein: 11-32 # features per peptide: 1-1 INFO [2024-12-24 03:00:14] C1 C2 C3 C4 C5 C6 # runs 3 3 3 3 3 3 # bioreplicates 1 1 1 1 1 1 # tech. replicates 3 3 3 3 3 3 INFO [2024-12-24 03:00:14] Some features are completely missing in at least one condition: D.GPLTGTYR_23_23_NA_NA, F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA, G.PLTGTYR_8_8_NA_NA, H.SFNVEYDDSQDK_465_465_NA_NA, K.AVVQDPALKPL_156_156_NA_NA ... INFO [2024-12-24 03:00:14] == Start the summarization per subplot... INFO [2024-12-24 03:00:18] == Summarization is done. test_dataProcess.R............ 0 tests test_dataProcess.R............ 1 tests [0;32mOK[0m test_dataProcess.R............ 2 tests [0;32mOK[0m [0;34m8.2s[0m INFO [2024-12-24 03:00:18] ** Features with one or two measurements across runs are removed. INFO [2024-12-24 03:00:18] ** Fractionation handled. INFO [2024-12-24 03:00:18] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-24 03:00:18] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-12-24 03:00:18] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-12-24 03:00:18] ** Use all features that the dataset originally has. INFO [2024-12-24 03:00:18] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-12-24 03:00:18] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-12-24 03:00:18] == Start the summarization per subplot... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-12-24 03:00:18] == Summarization is done. test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests test_groupComparison.R........ 0 tests INFO [2024-12-24 03:00:18] == Start to test and get inference in whole plot ... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-12-24 03:00:18] == Comparisons for all proteins are done. test_groupComparison.R........ 0 tests INFO [2024-12-24 03:00:18] == Start to test and get inference in whole plot ... INFO [2024-12-24 03:00:22] == Comparisons for all proteins are done. test_groupComparison.R........ 0 tests test_groupComparison.R........ 1 tests [0;32mOK[0m [0;34m4.3s[0m test_groupComparisonQCPlots.R. 0 tests test_groupComparisonQCPlots.R. 0 tests test_groupComparisonQCPlots.R. 0 tests INFO [2024-12-24 03:00:22] ** Features with one or two measurements across runs are removed. INFO [2024-12-24 03:00:22] ** Fractionation handled. INFO [2024-12-24 03:00:22] ** Updated quantification data to make balanced design. Missing values are marked by NA INFO [2024-12-24 03:00:22] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. INFO [2024-12-24 03:00:22] ** Log2 intensities = NA were considered as censored missing values. INFO [2024-12-24 03:00:22] ** Use all features that the dataset originally has. INFO [2024-12-24 03:00:22] # proteins: 2 # peptides per protein: 2-2 # features per peptide: 3-3 INFO [2024-12-24 03:00:22] 1 2 3 4 5 6 7 8 9 10 # runs 3 3 3 3 3 3 3 3 3 3 # bioreplicates 3 3 3 3 3 3 3 3 3 3 # tech. replicates 1 1 1 1 1 1 1 1 1 1 INFO [2024-12-24 03:00:22] == Start the summarization per subplot... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-12-24 03:00:22] == Summarization is done. test_groupComparisonQCPlots.R. 0 tests test_groupComparisonQCPlots.R. 0 tests test_groupComparisonQCPlots.R. 0 tests test_groupComparisonQCPlots.R. 0 tests INFO [2024-12-24 03:00:22] == Start to test and get inference in whole plot ... | | | 0% | |=================================== | 50% | |======================================================================| 100% INFO [2024-12-24 03:00:22] == Comparisons for all proteins are done. test_groupComparisonQCPlots.R. 0 tests Test passed 🥳 test_groupComparisonQCPlots.R. 8 tests [0;32mOK[0m [0;34m0.7s[0m [0;36m2ms[0m test_utils_groupcomparison_checks.R 0 tests test_utils_groupcomparison_checks.R 1 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 1 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 2 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 2 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 3 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 3 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 4 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 4 tests [0;32mOK[0m test_utils_groupcomparison_checks.R 5 tests [0;32mOK[0m [0;36m13ms[0m All ok, 17 results (13.3s) There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 4.93 0.37 16.68
MSstats.Rcheck/MSstats-Ex.timings
name | user | system | elapsed | |
DDARawData | 0.02 | 0.00 | 0.02 | |
DDARawData.Skyline | 0.01 | 0.00 | 0.02 | |
DIANNtoMSstatsFormat | 0 | 0 | 0 | |
DIARawData | 0 | 0 | 0 | |
DIAUmpiretoMSstatsFormat | 0.2 | 0.0 | 0.2 | |
FragPipetoMSstatsFormat | 0.06 | 0.00 | 0.06 | |
MSstatsGroupComparison | 0.34 | 0.00 | 0.35 | |
MSstatsGroupComparisonOutput | 0.55 | 0.00 | 0.54 | |
MSstatsGroupComparisonSingleProtein | 0.19 | 0.02 | 0.21 | |
MSstatsHandleMissing | 0.08 | 0.00 | 0.07 | |
MSstatsMergeFractions | 0.03 | 0.03 | 0.07 | |
MSstatsNormalize | 0.06 | 0.04 | 0.11 | |
MSstatsPrepareForDataProcess | 0.05 | 0.03 | 0.07 | |
MSstatsPrepareForGroupComparison | 0.17 | 0.02 | 0.21 | |
MSstatsPrepareForSummarization | 0.05 | 0.00 | 0.06 | |
MSstatsSelectFeatures | 0.26 | 0.02 | 1.02 | |
MSstatsSummarizationOutput | 0.33 | 0.01 | 0.34 | |
MSstatsSummarize | 0.28 | 0.02 | 0.33 | |
MSstatsSummarizeSingleLinear | 0.11 | 0.01 | 0.14 | |
MSstatsSummarizeSingleTMP | 0.13 | 0.00 | 0.12 | |
MSstatsSummarizeWithSingleCore | 0.32 | 0.03 | 0.36 | |
MaxQtoMSstatsFormat | 0.21 | 0.02 | 0.22 | |
OpenMStoMSstatsFormat | 0.09 | 0.00 | 0.10 | |
OpenSWATHtoMSstatsFormat | 0.08 | 0.00 | 0.07 | |
PDtoMSstatsFormat | 0.06 | 0.03 | 0.10 | |
ProgenesistoMSstatsFormat | 0.06 | 0.00 | 0.06 | |
SDRFtoAnnotation | 0.02 | 0.00 | 0.02 | |
SRMRawData | 0 | 0 | 0 | |
SkylinetoMSstatsFormat | 0.09 | 0.03 | 0.12 | |
SpectronauttoMSstatsFormat | 0.08 | 0.00 | 0.08 | |
checkRepeatedDesign | 0.19 | 0.00 | 0.19 | |
dataProcess | 0.55 | 0.02 | 0.56 | |
dataProcessPlots | 7.07 | 0.12 | 7.20 | |
designSampleSize | 0.30 | 0.02 | 0.31 | |
designSampleSizePlots | 0.33 | 0.03 | 0.36 | |
dot-makeQCPlot | 6.06 | 0.08 | 6.14 | |
example_SDRF | 0.00 | 0.01 | 0.02 | |
extractSDRF | 0.13 | 0.00 | 0.17 | |
getProcessed | 0.04 | 0.00 | 0.06 | |
getSamplesInfo | 0.33 | 0.03 | 0.36 | |
groupComparison | 0.34 | 0.02 | 0.36 | |
groupComparisonPlots | 3.50 | 0.09 | 3.59 | |
groupComparisonQCPlots | 0.80 | 0.02 | 0.81 | |
makePeptidesDictionary | 0 | 0 | 0 | |
modelBasedQCPlots | 0.81 | 0.00 | 0.81 | |
quantification | 0.25 | 0.01 | 0.27 | |