Anthony Wu
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/MSstatsLiP |
| git_branch: devel |
| git_last_commit: 0e254a4 |
| git_last_commit_date: 2025-05-27 10:37:56 -0400 (Tue, 27 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1374/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsLiP 1.15.1 (landing page) Anthony Wu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.15.1 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MSstatsLiP_1.15.1.tar.gz |
| StartedAt: 2025-08-15 05:36:49 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 05:41:37 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 288.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsLiP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MSstatsLiP_1.15.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/MSstatsLiP.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsLiP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsLiP' version '1.15.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MSstatsLiP' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.savePlotlyPlotHTML: no visible global function definition for
'txtProgressBar'
.savePlotlyPlotHTML: no visible global function definition for
'setTxtProgressBar'
.savePlotlyPlotHTML: no visible global function definition for 'zip'
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
'Sequence'
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'
StructuralBarcodePlotLiP: no visible binding for global variable
'Sequence'
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 Sequence
setTxtProgressBar sig txtProgressBar uniprot_iso zip
Consider adding
importFrom("utils", "setTxtProgressBar", "txtProgressBar", "zip")
to your NAMESPACE file.
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/MSstatsLiP/libs/x64/MSstatsLiP.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
dataProcessPlotsLiP 32.72 0.34 33.11
StructuralBarcodePlotLiP 5.76 0.15 5.92
* 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 NOTEs
See
'F:/biocbuild/bbs-3.22-bioc/meat/MSstatsLiP.Rcheck/00check.log'
for details.
MSstatsLiP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL MSstatsLiP ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'MSstatsLiP' ... ** this is package 'MSstatsLiP' version '1.15.1' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/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-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/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 MSstatsLiP.dll tmp.def RcppExports.o model_adjustment.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-MSstatsLiP/00new/MSstatsLiP/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 (MSstatsLiP)
MSstatsLiP.Rcheck/tests/tinytest.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 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("MSstatsLiP")
+ }
test_SkylinetoMSstatsLiPFormat.R 0 tests
test_SkylinetoMSstatsLiPFormat.R 1 tests [0;32mOK[0m
test_SkylinetoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
test_SkylinetoMSstatsLiPFormat.R 3 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 4 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 5 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 6 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 7 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 8 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 9 tests [0;32mOK[0m INFO [2025-08-15 05:40:32] ** Raw data from Skyline imported successfully.
INFO [2025-08-15 05:40:32] ** Raw data from Skyline cleaned successfully.
INFO [2025-08-15 05:40:32] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 10 tests [0;32mOK[0m [0;34m0.6s[0m
test_SpectronauttoMSstatsLiPFormat.R 0 tests
test_SpectronauttoMSstatsLiPFormat.R 0 tests
test_SpectronauttoMSstatsLiPFormat.R 1 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2025-08-15 05:40:33] ** Raw data from Spectronaut imported successfully.
INFO [2025-08-15 05:40:33] ** Raw data from Spectronaut cleaned successfully.
INFO [2025-08-15 05:40:33] ** Using annotation extracted from quantification data.
INFO [2025-08-15 05:40:33] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:40:33] ** 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 [2025-08-15 05:40:33] ** PGQvalue not found in input columns.
INFO [2025-08-15 05:40:33] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with NA
INFO [2025-08-15 05:40:33] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:40:33] ** Shared peptides are removed.
INFO [2025-08-15 05:40:33] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:40:33] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:40:33] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:40:33] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:40:33] ** Fractionation handled.
INFO [2025-08-15 05:40:33] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:40:33] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
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 [2025-08-15 05:40:33] ** Raw data from Spectronaut imported successfully.
INFO [2025-08-15 05:40:33] ** Raw data from Spectronaut cleaned successfully.
INFO [2025-08-15 05:40:33] ** Using annotation extracted from quantification data.
INFO [2025-08-15 05:40:33] ** 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;34m1.0s[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;34m32.4s[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;34m0.2s[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 [2025-08-15 05:41:06] == Start to test and get inference in whole plot ...
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INFO [2025-08-15 05:41:07] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2025-08-15 05:41:07] == Start to test and get inference in whole plot ...
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INFO [2025-08-15 05:41:07] == 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;34m1.5s[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;34m5.0s[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;34m12.1s[0m
All ok, 111 results (52.8s)
Warning message:
In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
>
> proc.time()
user system elapsed
59.82 1.28 61.09
MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsLiPFormat | 0.02 | 0.00 | 0.01 | |
| LiPRawData | 0.00 | 0.01 | 0.01 | |
| MSstatsLiP_Summarized | 0.01 | 0.00 | 0.01 | |
| MSstatsLiP_data | 0 | 0 | 0 | |
| MSstatsLiP_model | 0.02 | 0.00 | 0.02 | |
| PCAPlotLiP | 2.14 | 0.03 | 2.17 | |
| ResistanceBarcodePlotLiP | 0 | 0 | 0 | |
| SkylineTest | 0 | 0 | 0 | |
| SkylinetoMSstatsLiPFormat | 0 | 0 | 0 | |
| SpectronauttoMSstatsLiPFormat | 0.35 | 0.00 | 0.35 | |
| StructuralBarcodePlotLiP | 5.76 | 0.15 | 5.92 | |
| TrPRawData | 0 | 0 | 0 | |
| annotSite | 0 | 0 | 0 | |
| calculateProteolyticResistance | 0 | 0 | 0 | |
| calculateTrypticity | 0.02 | 0.01 | 0.03 | |
| correlationPlotLiP | 0.45 | 0.00 | 0.45 | |
| dataProcessPlotsLiP | 32.72 | 0.34 | 33.11 | |
| dataSummarizationLiP | 0.79 | 0.05 | 0.84 | |
| groupComparisonLiP | 0.71 | 0.00 | 0.71 | |
| groupComparisonPlotsLiP | 2.34 | 0.05 | 2.42 | |
| locateMod | 0 | 0 | 0 | |
| locatePTM | 0.09 | 0.00 | 0.10 | |
| raw_lip | 0.07 | 0.00 | 0.06 | |
| raw_prot | 0.06 | 0.01 | 0.08 | |
| tidyFasta | 0.03 | 0.00 | 0.05 | |
| trypticHistogramLiP | 0.41 | 0.00 | 0.40 | |