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This page was generated on 2024-03-29 11:37:58 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 1345/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLiP 1.8.2  (landing page)
Devon Kohler
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/MSstatsLiP
git_branch: RELEASE_3_18
git_last_commit: 177b0db
git_last_commit_date: 2024-03-19 13:52:22 -0400 (Tue, 19 Mar 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MSstatsLiP on merida1


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: 1.8.2
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_1.8.2.tar.gz
StartedAt: 2024-03-28 05:53:41 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 06:01:42 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 480.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MSstatsLiP.Rcheck
Warnings: NA

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_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/MSstatsLiP.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLiP’ version ‘1.8.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsLiP’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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 ... 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      47.823  0.313  53.427
StructuralBarcodePlotLiP  8.721  0.098  10.292
* 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:
   call| -->    address = FALSE))
   diff| Execution was not silent. A warning was thrown with message
   diff| 'No shared levels found between `names(values)` of the manual scale and the
   diff| data's fill values.'
  ----- FAILED[xcpt]: test_trypticHistogramLiP.R<50--52>
   call| expect_silent(StructuralBarcodePlotLiP(MSstatsLiP_model, "../extdata/ExampleFastaFile.fasta", 
   call| -->    which.prot = "P36112"))
   diff| Execution was not silent. A warning was thrown with message
   diff| 'No shared levels found between `names(values)` of the manual scale and the
   diff| data's fill values.'
  Error: 2 out of 111 tests failed
  In addition: Warning message:
  In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
    no non-missing arguments to max; returning -Inf
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/Resources/library’
* installing *source* package ‘MSstatsLiP’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c model_adjustment.cpp -o model_adjustment.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/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.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests OK INFO  [2024-03-28 05:59:48] ** Raw data from Skyline imported successfully.
INFO  [2024-03-28 05:59:48] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-28 05:59:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R   10 tests OK 0.9s

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 05:59:49] ** Raw data from Spectronaut imported successfully.
INFO  [2024-03-28 05:59:49] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-03-28 05:59:49] ** Using annotation extracted from quantification data.
INFO  [2024-03-28 05:59:49] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-28 05:59:49] ** 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 05:59:49] ** PGQvalue not found in input columns.
INFO  [2024-03-28 05:59:49] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2024-03-28 05:59:49] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-28 05:59:49] ** Shared peptides are removed.
INFO  [2024-03-28 05:59:49] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-28 05:59:49] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-28 05:59:49] ** Run annotation merged with quantification data.
INFO  [2024-03-28 05:59:49] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-28 05:59:49] ** Fractionation handled.
INFO  [2024-03-28 05:59:49] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-28 05:59:49] ** 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 05:59:50] ** Raw data from Spectronaut imported successfully.
INFO  [2024-03-28 05:59:50] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-03-28 05:59:50] ** Using annotation extracted from quantification data.
INFO  [2024-03-28 05:59:50] ** 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 1.5s

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 52.9s

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 0.4s

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 06:00:44]  == Start to test and get inference in whole plot ...

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INFO  [2024-03-28 06:00:44]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2024-03-28 06:00:44]  == Start to test and get inference in whole plot ...

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INFO  [2024-03-28 06:00:44]  == 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 1.4s

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 9.2s

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 1 fails 
test_trypticHistogramLiP.R....   13 tests 2 fails 
test_trypticHistogramLiP.R....   14 tests 2 fails 
test_trypticHistogramLiP.R....   15 tests 2 fails 
test_trypticHistogramLiP.R....   16 tests 2 fails 
test_trypticHistogramLiP.R....   17 tests 2 fails 
test_trypticHistogramLiP.R....   18 tests 2 fails 
test_trypticHistogramLiP.R....   19 tests 2 fails 
test_trypticHistogramLiP.R....   20 tests 2 fails 
test_trypticHistogramLiP.R....   21 tests 2 fails 
test_trypticHistogramLiP.R....   22 tests 2 fails 
test_trypticHistogramLiP.R....   23 tests 2 fails 
test_trypticHistogramLiP.R....   24 tests 2 fails 
test_trypticHistogramLiP.R....   25 tests 2 fails 16.9s
----- FAILED[xcpt]: test_trypticHistogramLiP.R<45--47>
 call| expect_silent(StructuralBarcodePlotLiP(MSstatsLiP_model, "../extdata/ExampleFastaFile.fasta", 
 call| -->    address = FALSE))
 diff| Execution was not silent. A warning was thrown with message
 diff| 'No shared levels found between `names(values)` of the manual scale and the
 diff| data's fill values.'
----- FAILED[xcpt]: test_trypticHistogramLiP.R<50--52>
 call| expect_silent(StructuralBarcodePlotLiP(MSstatsLiP_model, "../extdata/ExampleFastaFile.fasta", 
 call| -->    which.prot = "P36112"))
 diff| Execution was not silent. A warning was thrown with message
 diff| 'No shared levels found between `names(values)` of the manual scale and the
 diff| data's fill values.'
Error: 2 out of 111 tests failed
In addition: Warning message:
In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Execution halted

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

nameusersystemelapsed
DIANNtoMSstatsLiPFormat0.0390.0060.051
LiPRawData0.0200.0040.029
MSstatsLiP_Summarized0.0340.0070.048
MSstatsLiP_data0.0150.0040.021
MSstatsLiP_model0.0320.0070.047
PCAPlotLiP3.6460.1004.213
ResistanceBarcodePlotLiP0.0020.0010.003
SkylineTest0.0130.0030.016
SkylinetoMSstatsLiPFormat0.0160.0040.022
SpectronauttoMSstatsLiPFormat0.4390.0280.533
StructuralBarcodePlotLiP 8.721 0.09810.292
TrPRawData0.0180.0040.026
annotSite0.0020.0000.003
calculateProteolyticResistance0.0150.0010.017
calculateTrypticity0.0300.0040.039
correlationPlotLiP0.6020.0070.692
dataProcessPlotsLiP47.823 0.31353.427
dataSummarizationLiP1.0340.0331.076
groupComparisonLiP0.9340.0200.965
groupComparisonPlotsLiP3.2430.0454.566
locateMod0.0010.0010.001
locatePTM0.1180.0040.709
raw_lip0.1050.0040.109
raw_prot0.1110.0050.118
tidyFasta0.0490.0020.051
trypticHistogramLiP0.5730.0110.794