Multiple platform build/check report for BioC 3.19 - CHECK results for MSstatsLiP on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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*

CHECK results for MSstatsLiP on kjohnson3

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.

raw results

Summary

Package: MSstatsLiP

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsLiP_1.10.0.tar.gz

StartedAt: 2024-06-10 23:09:47 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 23:15:18 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 330.8 seconds

RetCode: 0

Status: OK

CheckDir: MSstatsLiP.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsLiP_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstatsLiP.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLiP’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsLiP’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 25.174  0.331  36.733
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/MSstatsLiP.Rcheck/00check.log’
for details.

Installation output

MSstatsLiP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsLiP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MSstatsLiP’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c model_adjustment.cpp -o model_adjustment.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MSstatsLiP.so RcppExports.o model_adjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)

Tests output

MSstatsLiP.Rcheck/tests/tinytest.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+   tinytest::test_package("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  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests [0;32mOK[0m INFO  [2024-06-10 23:14:00] ** Raw data from Skyline imported successfully.
INFO  [2024-06-10 23:14:00] ** Raw data from Skyline cleaned successfully.
INFO  [2024-06-10 23:14:00] ** 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    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  [2024-06-10 23:14:01] ** Raw data from Spectronaut imported successfully.
INFO  [2024-06-10 23:14:01] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-06-10 23:14:01] ** Using annotation extracted from quantification data.
INFO  [2024-06-10 23:14:01] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-06-10 23:14:01] ** 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  [2024-06-10 23:14:01] ** PGQvalue not found in input columns.
INFO  [2024-06-10 23:14:01] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2024-06-10 23:14:01] ** Features with all missing measurements across runs are removed.
INFO  [2024-06-10 23:14:01] ** Shared peptides are removed.
INFO  [2024-06-10 23:14:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-06-10 23:14:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-06-10 23:14:01] ** Run annotation merged with quantification data.
INFO  [2024-06-10 23:14:01] ** Features with one or two measurements across runs are removed.
INFO  [2024-06-10 23:14:01] ** Fractionation handled.
INFO  [2024-06-10 23:14:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-06-10 23:14:01] ** 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  [2024-06-10 23:14:01] ** Raw data from Spectronaut imported successfully.
INFO  [2024-06-10 23:14:01] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-06-10 23:14:01] ** Using annotation extracted from quantification data.
INFO  [2024-06-10 23:14:01] ** 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;34m1.5s[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;34m37.9s[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;34m0.3s[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  [2024-06-10 23:14:40]  == Start to test and get inference in whole plot ...

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INFO  [2024-06-10 23:14:40]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2024-06-10 23:14:40]  == Start to test and get inference in whole plot ...

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INFO  [2024-06-10 23:14:41]  == 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;34m1.3s[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;34m7.2s[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;34m12.2s[0m
All ok, 111 results (1m 1.1s)
Warning message:
In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
> 
> proc.time()
   user  system elapsed 
 48.409   1.112  71.974

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

name	user	system	elapsed
DIANNtoMSstatsLiPFormat	0.059	0.003	0.106
LiPRawData	0.008	0.001	0.013
MSstatsLiP_Summarized	0.016	0.003	0.036
MSstatsLiP_data	0.007	0.001	0.016
MSstatsLiP_model	0.015	0.002	0.030
PCAPlotLiP	1.849	0.066	3.133
ResistanceBarcodePlotLiP	0.001	0.001	0.002
SkylineTest	0.006	0.001	0.013
SkylinetoMSstatsLiPFormat	0.008	0.001	0.018
SpectronauttoMSstatsLiPFormat	1.100	0.026	1.651
StructuralBarcodePlotLiP	3.505	0.061	4.922
TrPRawData	0.008	0.001	0.010
annotSite	0.001	0.000	0.001
calculateProteolyticResistance	0.010	0.002	0.019
calculateTrypticity	0.017	0.002	0.028
correlationPlotLiP	0.283	0.005	0.374
dataProcessPlotsLiP	25.174	0.331	36.733
dataSummarizationLiP	0.881	0.019	1.349
groupComparisonLiP	1.281	0.021	1.821
groupComparisonPlotsLiP	1.501	0.031	2.300
locateMod	0.001	0.000	0.000
locatePTM	0.067	0.003	0.094
raw_lip	0.054	0.002	0.092
raw_prot	0.054	0.002	0.091
tidyFasta	0.059	0.003	0.096
trypticHistogramLiP	0.280	0.006	0.469