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This page was generated on 2024-03-28 11:38:06 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1345/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLiP 1.9.2  (landing page)
Devon Kohler
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/MSstatsLiP
git_branch: devel
git_last_commit: 18e367a
git_last_commit_date: 2024-03-19 13:50:28 -0400 (Tue, 19 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for MSstatsLiP on palomino3


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: 1.9.2
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MSstatsLiP_1.9.2.tar.gz
StartedAt: 2024-03-28 04:26:15 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 04:30:31 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 256.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsLiP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MSstatsLiP_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MSstatsLiP.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 'MSstatsLiP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsLiP' version '1.9.2'
* 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) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-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 25.59   0.36   25.95
* 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-3.19-bioc/meat/MSstatsLiP.Rcheck/00check.log'
for details.

Installation output

MSstatsLiP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MSstatsLiP
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'MSstatsLiP' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c model_adjustment.cpp -o model_adjustment.o
g++ -std=gnu++17 -shared -s -static-libgcc -o MSstatsLiP.dll tmp.def RcppExports.o model_adjustment.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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)

Tests output

MSstatsLiP.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2024-03-16 r86144 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("MSstatsLiP")
+ }

test_SkylinetoMSstatsLiPFormat.R    0 tests    
test_SkylinetoMSstatsLiPFormat.R    1 tests OK 
test_SkylinetoMSstatsLiPFormat.R    2 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R   10 tests OK 0.5s

test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    1 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    2 tests OK INFO  [2024-03-28 04:29:38] ** Raw data from Spectronaut imported successfully.
INFO  [2024-03-28 04:29:38] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-03-28 04:29:38] ** Using annotation extracted from quantification data.
INFO  [2024-03-28 04:29:38] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-28 04:29:38] ** 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  [2024-03-28 04:29:38] ** PGQvalue not found in input columns.
INFO  [2024-03-28 04:29:38] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2024-03-28 04:29:38] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-28 04:29:38] ** Shared peptides are removed.
INFO  [2024-03-28 04:29:38] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-28 04:29:38] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-28 04:29:38] ** Run annotation merged with quantification data.
INFO  [2024-03-28 04:29:38] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-28 04:29:38] ** Fractionation handled.
INFO  [2024-03-28 04:29:38] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-28 04:29:38] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_SpectronauttoMSstatsLiPFormat.R    3 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    4 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    5 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    6 tests OK INFO  [2024-03-28 04:29:39] ** Raw data from Spectronaut imported successfully.
INFO  [2024-03-28 04:29:39] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-03-28 04:29:39] ** Using annotation extracted from quantification data.
INFO  [2024-03-28 04:29:39] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_SpectronauttoMSstatsLiPFormat.R    7 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    8 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    9 tests OK 0.9s

test_dataProcessPlotsLiP.R....    0 tests    
test_dataProcessPlotsLiP.R....    1 tests OK 
test_dataProcessPlotsLiP.R....    2 tests OK 
test_dataProcessPlotsLiP.R....    3 tests OK 
test_dataProcessPlotsLiP.R....    4 tests OK 
test_dataProcessPlotsLiP.R....    5 tests OK 
test_dataProcessPlotsLiP.R....    6 tests OK 
test_dataProcessPlotsLiP.R....    7 tests OK 
test_dataProcessPlotsLiP.R....    8 tests OK 
test_dataProcessPlotsLiP.R....    9 tests OK 
test_dataProcessPlotsLiP.R....   10 tests OK 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 OK 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 OK 24.8s

test_dataSummarizationLiP.R...    0 tests    
test_dataSummarizationLiP.R...    0 tests    
test_dataSummarizationLiP.R...    1 tests OK 
test_dataSummarizationLiP.R...    2 tests OK 
test_dataSummarizationLiP.R...    3 tests OK 
test_dataSummarizationLiP.R...    4 tests OK 
test_dataSummarizationLiP.R...    5 tests OK 
test_dataSummarizationLiP.R...    6 tests OK 
test_dataSummarizationLiP.R...    7 tests OK 
test_dataSummarizationLiP.R...    8 tests OK 
test_dataSummarizationLiP.R...    9 tests OK 
test_dataSummarizationLiP.R...   10 tests OK 
test_dataSummarizationLiP.R...   11 tests OK 
test_dataSummarizationLiP.R...   12 tests OK 
test_dataSummarizationLiP.R...   13 tests OK 
test_dataSummarizationLiP.R...   14 tests OK 
test_dataSummarizationLiP.R...   15 tests OK 
test_dataSummarizationLiP.R...   16 tests OK 
test_dataSummarizationLiP.R...   17 tests OK 
test_dataSummarizationLiP.R...   18 tests OK 
test_dataSummarizationLiP.R...   19 tests OK 
test_dataSummarizationLiP.R...   20 tests OK 
test_dataSummarizationLiP.R...   21 tests OK 
test_dataSummarizationLiP.R...   22 tests OK 
test_dataSummarizationLiP.R...   23 tests OK 
test_dataSummarizationLiP.R...   24 tests OK 
test_dataSummarizationLiP.R...   25 tests OK 
test_dataSummarizationLiP.R...   26 tests OK 
test_dataSummarizationLiP.R...   27 tests OK 
test_dataSummarizationLiP.R...   28 tests OK Starting PTM summarization...

test_dataSummarizationLiP.R...   29 tests OK 0.1s

test_groupComparisonLiP.R.....    0 tests    
test_groupComparisonLiP.R.....    0 tests    
test_groupComparisonLiP.R.....    1 tests OK 
test_groupComparisonLiP.R.....    2 tests OK Starting PTM modeling...

test_groupComparisonLiP.R.....    3 tests OK Starting PTM modeling...
INFO  [2024-03-28 04:30:04]  == Start to test and get inference in whole plot ...

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INFO  [2024-03-28 04:30:04]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2024-03-28 04:30:04]  == Start to test and get inference in whole plot ...

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INFO  [2024-03-28 04:30:04]  == Comparisons for all proteins are done.
Starting adjustment...

test_groupComparisonLiP.R.....    3 tests OK 
test_groupComparisonLiP.R.....    4 tests OK 
test_groupComparisonLiP.R.....    5 tests OK 
test_groupComparisonLiP.R.....    6 tests OK 
test_groupComparisonLiP.R.....    7 tests OK 
test_groupComparisonLiP.R.....    8 tests OK 
test_groupComparisonLiP.R.....    9 tests OK 
test_groupComparisonLiP.R.....   10 tests OK 0.6s

test_groupComparisonPlotsLiP.R    0 tests    
test_groupComparisonPlotsLiP.R    1 tests OK 
test_groupComparisonPlotsLiP.R    2 tests OK 
test_groupComparisonPlotsLiP.R    3 tests OK 
test_groupComparisonPlotsLiP.R    4 tests OK 
test_groupComparisonPlotsLiP.R    5 tests OK 
test_groupComparisonPlotsLiP.R    6 tests OK 
test_groupComparisonPlotsLiP.R    7 tests OK 
test_groupComparisonPlotsLiP.R    8 tests OK 
test_groupComparisonPlotsLiP.R    9 tests OK 
test_groupComparisonPlotsLiP.R   10 tests OK 
test_groupComparisonPlotsLiP.R   11 tests OK 
test_groupComparisonPlotsLiP.R   12 tests OK 
test_groupComparisonPlotsLiP.R   13 tests OK 
test_groupComparisonPlotsLiP.R   14 tests OK 
test_groupComparisonPlotsLiP.R   15 tests OK 
test_groupComparisonPlotsLiP.R   16 tests OK 4.2s

test_trypticHistogramLiP.R....    0 tests    
test_trypticHistogramLiP.R....    0 tests    
test_trypticHistogramLiP.R....    0 tests    
test_trypticHistogramLiP.R....    1 tests OK 
test_trypticHistogramLiP.R....    2 tests OK 
test_trypticHistogramLiP.R....    3 tests OK 
test_trypticHistogramLiP.R....    4 tests OK 
test_trypticHistogramLiP.R....    5 tests OK 
test_trypticHistogramLiP.R....    6 tests OK 
test_trypticHistogramLiP.R....    7 tests OK 
test_trypticHistogramLiP.R....    8 tests OK 
test_trypticHistogramLiP.R....    9 tests OK 
test_trypticHistogramLiP.R....   10 tests OK 
test_trypticHistogramLiP.R....   11 tests OK 
test_trypticHistogramLiP.R....   12 tests OK 
test_trypticHistogramLiP.R....   13 tests OK 
test_trypticHistogramLiP.R....   14 tests OK 
test_trypticHistogramLiP.R....   15 tests OK 
test_trypticHistogramLiP.R....   16 tests OK 
test_trypticHistogramLiP.R....   17 tests OK 
test_trypticHistogramLiP.R....   18 tests OK 
test_trypticHistogramLiP.R....   19 tests OK 
test_trypticHistogramLiP.R....   20 tests OK 
test_trypticHistogramLiP.R....   21 tests OK 
test_trypticHistogramLiP.R....   22 tests OK 
test_trypticHistogramLiP.R....   23 tests OK 
test_trypticHistogramLiP.R....   24 tests OK 
test_trypticHistogramLiP.R....   25 tests OK 10.0s
All ok, 111 results (41.1s)
Warning message:
In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
> 
> proc.time()
   user  system elapsed 
  46.98    1.29   48.23

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsLiPFormat0.010.000.02
LiPRawData000
MSstatsLiP_Summarized0.020.000.02
MSstatsLiP_data0.000.010.02
MSstatsLiP_model0.010.000.01
PCAPlotLiP1.910.102.02
ResistanceBarcodePlotLiP000
SkylineTest0.010.000.01
SkylinetoMSstatsLiPFormat000
SpectronauttoMSstatsLiPFormat0.690.030.72
StructuralBarcodePlotLiP3.410.033.44
TrPRawData0.010.000.01
annotSite000
calculateProteolyticResistance0.020.000.02
calculateTrypticity0.030.000.03
correlationPlotLiP0.380.000.38
dataProcessPlotsLiP25.59 0.3625.95
dataSummarizationLiP0.780.010.80
groupComparisonLiP1.080.001.07
groupComparisonPlotsLiP1.800.001.81
locateMod000
locatePTM0.050.020.07
raw_lip0.060.020.07
raw_prot0.050.000.05
tidyFasta0.030.000.03
trypticHistogramLiP0.330.000.33