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This page was generated on 2022-01-21 11:08:05 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 riesling1


To the developers/maintainers of the MSstatsLiP package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1224/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLiP 1.1.0  (landing page)
Devon Kohler
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/MSstatsLiP
git_branch: master
git_last_commit: b30c523
git_last_commit_date: 2021-10-26 13:13:30 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'MSstats' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'MSstats' which is not available

Summary

Package: MSstatsLiP
Version: 1.1.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSstatsLiP_1.1.0.tar.gz
StartedAt: 2022-01-20 19:29:00 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:32:31 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 211.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsLiP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MSstatsLiP_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MSstatsLiP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSstatsLiP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsLiP' version '1.1.0'
* 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 'MSstatsLiP' can be installed ... OK
* 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 R 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 ... OK
* 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 'D:/biocbuild/bbs-3.15-bioc/R/library/MSstatsLiP/libs/x64/MSstatsLiP.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 22.47   0.11   22.58
BarcodePlotLiP       7.69   0.12    7.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/MSstatsLiP.Rcheck/00check.log'
for details.



Installation output

MSstatsLiP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MSstatsLiP
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MSstatsLiP' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c model_adjustment.cpp -o model_adjustment.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MSstatsLiP.dll tmp.def RcppExports.o model_adjustment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
  converting help for package 'MSstatsLiP'
    finding HTML links ... done
    BarcodePlotLiP                          html  
    LiPRawData                              html  
    MSstatsLiP                              html  
    MSstatsLiP_Summarized                   html  
    MSstatsLiP_data                         html  
    MSstatsLiP_model                        html  
    PCAPlotLiP                              html  
    SkylineTest                             html  
    SkylinetoMSstatsLiPFormat               html  
    SpectronauttoMSstatsLiPFormat           html  
    TrPRawData                              html  
    annotSite                               html  
    calculateTrypticity                     html  
    correlationPlotLiP                      html  
    dataProcessPlotsLiP                     html  
    dataSummarizationLiP                    html  
    groupComparisonLiP                      html  
    groupComparisonPlotsLiP                 html  
    locateMod                               html  
    locatePTM                               html  
    tidyFasta                               html  
    trypticHistogramLiP                     html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'mBPCR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Pi' is missing or broken
 done

Tests output

MSstatsLiP.Rcheck/tests/tinytest.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests OK INFO  [2022-01-20 19:31:46] ** Raw data from Skyline imported successfully.
INFO  [2022-01-20 19:31:46] ** Raw data from Skyline cleaned successfully.
INFO  [2022-01-20 19:31:46] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R   10 tests OK 0.6s

test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    1 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    2 tests OK INFO  [2022-01-20 19:31:47] ** Raw data from Spectronaut imported successfully.
INFO  [2022-01-20 19:31:47] ** Raw data from Spectronaut cleaned successfully.
INFO  [2022-01-20 19:31:47] ** Using annotation extracted from quantification data.
INFO  [2022-01-20 19:31:47] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2022-01-20 19:31:47] ** 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  [2022-01-20 19:31:47] ** PGQvalue not found in input columns.
INFO  [2022-01-20 19:31:47] ** Intensities with values smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2022-01-20 19:31:47] ** Features with all missing measurements across runs are removed.
INFO  [2022-01-20 19:31:47] ** Shared peptides are removed.
INFO  [2022-01-20 19:31:47] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2022-01-20 19:31:47] ** Features with one or two measurements across runs are removed.
INFO  [2022-01-20 19:31:47] ** Run annotation merged with quantification data.
INFO  [2022-01-20 19:31:47] ** Features with one or two measurements across runs are removed.
INFO  [2022-01-20 19:31:47] ** Fractionation handled.
INFO  [2022-01-20 19:31:47] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2022-01-20 19:31:47] ** 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  [2022-01-20 19:31:47] ** Raw data from Spectronaut imported successfully.
INFO  [2022-01-20 19:31:47] ** Raw data from Spectronaut cleaned successfully.
INFO  [2022-01-20 19:31:47] ** Using annotation extracted from quantification data.
INFO  [2022-01-20 19:31:47] ** 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 0.7s

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 18.7s

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  [2022-01-20 19:32:06]  == Start to test and get inference in whole plot ...

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INFO  [2022-01-20 19:32:06]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2022-01-20 19:32:06]  == Start to test and get inference in whole plot ...

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INFO  [2022-01-20 19:32:06]  == 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 0.5s

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 3.8s

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 9.2s
All ok, 111 results (33.5s)
Warning messages:
1: In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 1 has 0 rows but longest item has 1; filled with NA
3: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 3 has 0 rows but longest item has 1; filled with NA
4: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 4 has 0 rows but longest item has 1; filled with NA
5: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 1 has 0 rows but longest item has 1; filled with NA
6: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 2 has 0 rows but longest item has 1; filled with NA
7: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 3 has 0 rows but longest item has 1; filled with NA
8: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 1 has 0 rows but longest item has 1; filled with NA
9: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 2 has 0 rows but longest item has 1; filled with NA
10: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names,  :
  Item 3 has 0 rows but longest item has 1; filled with NA
> 
> proc.time()
   user  system elapsed 
  39.01    0.81   39.84 

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

nameusersystemelapsed
BarcodePlotLiP7.690.127.81
LiPRawData0.010.000.02
MSstatsLiP_Summarized0.020.000.02
MSstatsLiP_data000
MSstatsLiP_model000
PCAPlotLiP1.570.031.61
SkylineTest000
SkylinetoMSstatsLiPFormat000
SpectronauttoMSstatsLiPFormat0.190.050.23
TrPRawData000
annotSite000
calculateTrypticity0.020.000.02
correlationPlotLiP0.340.020.37
dataProcessPlotsLiP22.47 0.1122.58
dataSummarizationLiP0.580.060.64
groupComparisonLiP0.480.000.49
groupComparisonPlotsLiP1.750.001.75
locateMod000
locatePTM0.100.010.10
tidyFasta0.030.000.04
trypticHistogramLiP0.340.000.34