Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-04-02 19:29 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 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 1353/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLiP 1.12.0  (landing page)
Devon Kohler
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/MSstatsLiP
git_branch: RELEASE_3_20
git_last_commit: cb0fdf8
git_last_commit_date: 2024-10-29 11:05:42 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

CHECK results for MSstatsLiP on nebbiolo2

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: 1.12.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstatsLiP_1.12.0.tar.gz
StartedAt: 2025-04-01 00:16:20 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 00:20:03 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 223.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MSstatsLiP.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MSstatsLiP_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsLiP.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLiP’ version ‘1.12.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 20.483  0.241  20.727
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  test_trypticHistogramLiP.R....   24 tests OK 
  test_trypticHistogramLiP.R....   25 tests OK 7.5s
  ----- FAILED[xcpt]: test_SpectronauttoMSstatsLiPFormat.R<7--10>
   call| expect_silent(SpectronauttoMSstatsLiPFormat(LiPRawData, "../extdata/ExampleFastaFile.fasta", 
   call| -->    TrPRawData, use_log_file = FALSE, append = FALSE))
   diff| Execution was not silent. A warning was thrown with message
   diff| 'no non-missing arguments to max; returning -Inf'
  ----- FAILED[xcpt]: test_SpectronauttoMSstatsLiPFormat.R<13--16>
   call| expect_silent(SpectronauttoMSstatsLiPFormat(LiPRawData, "../extdata/ExampleFastaFile.fasta", 
   call| -->    use_log_file = FALSE, append = FALSE))
   diff| Execution was not silent. A warning was thrown with message
   diff| 'no non-missing arguments to max; returning -Inf'
  Error: 2 out of 111 tests failed
  In addition: There were 35 warnings (use warnings() to see them)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MSstatsLiP.Rcheck/00check.log’
for details.

Installation output

MSstatsLiP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MSstatsLiP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘MSstatsLiP’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c model_adjustment.cpp -o model_adjustment.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o MSstatsLiP.so RcppExports.o model_adjustment.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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.fail


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests OK INFO  [2025-04-01 00:18:50] ** Raw data from Skyline imported successfully.
INFO  [2025-04-01 00:18:50] ** Raw data from Skyline cleaned successfully.
INFO  [2025-04-01 00:18:50] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R   10 tests OK 0.4s

test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    1 tests 1 fails 
test_SpectronauttoMSstatsLiPFormat.R    2 tests 2 fails INFO  [2025-04-01 00:18:51] ** Raw data from Spectronaut imported successfully.
INFO  [2025-04-01 00:18:51] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-04-01 00:18:51] ** Using annotation extracted from quantification data.
INFO  [2025-04-01 00:18:51] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2025-04-01 00:18:51] ** 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  [2025-04-01 00:18:51] ** PGQvalue not found in input columns.
INFO  [2025-04-01 00:18:51] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with NA
INFO  [2025-04-01 00:18:51] ** Features with all missing measurements across runs are removed.
INFO  [2025-04-01 00:18:51] ** Shared peptides are removed.
INFO  [2025-04-01 00:18:51] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2025-04-01 00:18:51] ** Features with one or two measurements across runs are removed.
INFO  [2025-04-01 00:18:51] ** Run annotation merged with quantification data.
INFO  [2025-04-01 00:18:51] ** Features with one or two measurements across runs are removed.
INFO  [2025-04-01 00:18:51] ** Fractionation handled.
INFO  [2025-04-01 00:18:51] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2025-04-01 00:18:51] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_SpectronauttoMSstatsLiPFormat.R    3 tests 2 fails 
test_SpectronauttoMSstatsLiPFormat.R    4 tests 2 fails 
test_SpectronauttoMSstatsLiPFormat.R    5 tests 2 fails 
test_SpectronauttoMSstatsLiPFormat.R    6 tests 2 fails INFO  [2025-04-01 00:18:51] ** Raw data from Spectronaut imported successfully.
INFO  [2025-04-01 00:18:51] ** Raw data from Spectronaut cleaned successfully.
INFO  [2025-04-01 00:18:51] ** Using annotation extracted from quantification data.
INFO  [2025-04-01 00:18:51] ** Run labels were standardized to remove symbols such as '.' or '%'.

test_SpectronauttoMSstatsLiPFormat.R    7 tests 2 fails 
test_SpectronauttoMSstatsLiPFormat.R    8 tests 2 fails 
test_SpectronauttoMSstatsLiPFormat.R    9 tests 2 fails 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 20.9s

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 0.2s

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  [2025-04-01 00:19:12]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===============                                                       |  21%
  |                                                                            
  |====================                                                  |  29%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |==============================                                        |  43%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |========================================                              |  57%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==================================================                    |  71%
  |                                                                            
  |=======================================================               |  79%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-04-01 00:19:13]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2025-04-01 00:19:13]  == Start to test and get inference in whole plot ...

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=====                                                                 |   8%
  |                                                                            
  |===========                                                           |  15%
  |                                                                            
  |================                                                      |  23%
  |                                                                            
  |======================                                                |  31%
  |                                                                            
  |===========================                                           |  38%
  |                                                                            
  |================================                                      |  46%
  |                                                                            
  |======================================                                |  54%
  |                                                                            
  |===========================================                           |  62%
  |                                                                            
  |================================================                      |  69%
  |                                                                            
  |======================================================                |  77%
  |                                                                            
  |===========================================================           |  85%
  |                                                                            
  |=================================================================     |  92%
  |                                                                            
  |======================================================================| 100%
INFO  [2025-04-01 00:19:13]  == 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 4.1s

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 7.5s
----- FAILED[xcpt]: test_SpectronauttoMSstatsLiPFormat.R<7--10>
 call| expect_silent(SpectronauttoMSstatsLiPFormat(LiPRawData, "../extdata/ExampleFastaFile.fasta", 
 call| -->    TrPRawData, use_log_file = FALSE, append = FALSE))
 diff| Execution was not silent. A warning was thrown with message
 diff| 'no non-missing arguments to max; returning -Inf'
----- FAILED[xcpt]: test_SpectronauttoMSstatsLiPFormat.R<13--16>
 call| expect_silent(SpectronauttoMSstatsLiPFormat(LiPRawData, "../extdata/ExampleFastaFile.fasta", 
 call| -->    use_log_file = FALSE, append = FALSE))
 diff| Execution was not silent. A warning was thrown with message
 diff| 'no non-missing arguments to max; returning -Inf'
Error: 2 out of 111 tests failed
In addition: There were 35 warnings (use warnings() to see them)
Execution halted

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsLiPFormat0.0350.0030.039
LiPRawData0.0070.0000.007
MSstatsLiP_Summarized0.0120.0010.012
MSstatsLiP_data0.0070.0000.007
MSstatsLiP_model0.0130.0000.013
PCAPlotLiP1.5490.1121.661
ResistanceBarcodePlotLiP0.0000.0010.001
SkylineTest0.0060.0010.006
SkylinetoMSstatsLiPFormat0.0050.0020.006
SpectronauttoMSstatsLiPFormat0.8550.0800.890
StructuralBarcodePlotLiP3.1120.0463.159
TrPRawData0.0060.0000.006
annotSite0.0010.0000.001
calculateProteolyticResistance0.0070.0010.008
calculateTrypticity0.0130.0000.014
correlationPlotLiP0.2340.0040.239
dataProcessPlotsLiP20.483 0.24120.727
dataSummarizationLiP0.6030.0240.590
groupComparisonLiP0.9490.0531.002
groupComparisonPlotsLiP1.3130.0021.314
locateMod0.0010.0000.000
locatePTM0.0610.0040.066
raw_lip0.0410.0050.047
raw_prot0.0440.0050.049
tidyFasta0.0210.0020.022
trypticHistogramLiP0.2630.0140.270