Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-20 12:05:37 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 nebbiolo1


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? 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 1261/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLiP 1.2.1  (landing page)
Devon Kohler
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/MSstatsLiP
git_branch: RELEASE_3_15
git_last_commit: 87a9dd6
git_last_commit_date: 2022-04-28 09:05:59 -0400 (Thu, 28 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsLiP
Version: 1.2.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSstatsLiP_1.2.1.tar.gz
StartedAt: 2022-05-19 20:30:35 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 20:33:59 -0400 (Thu, 19 May 2022)
EllapsedTime: 203.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsLiP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSstatsLiP_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MSstatsLiP.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLiP’ version ‘1.2.1’
* 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
* 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’ ... NOTE
The following files look like leftovers/mistakes:
  ‘MSstats_groupComparison_log_2022_04_22_12_09_48.log’
Please remove them from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
dataProcessPlotsLiP      20.211  0.172  20.384
StructuralBarcodePlotLiP  5.241  0.020   5.262
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/MSstatsLiP.Rcheck/00check.log’
for details.



Installation output

MSstatsLiP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MSstatsLiP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘MSstatsLiP’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c model_adjustment.cpp -o model_adjustment.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o MSstatsLiP.so RcppExports.o model_adjustment.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MSstatsLiP/00new/MSstatsLiP/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsLiP)

Tests output

MSstatsLiP.Rcheck/tests/tinytest.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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  [2022-05-19 20:33:18] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:18] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests OK INFO  [2022-05-19 20:33:18] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:18] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:18] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests OK INFO  [2022-05-19 20:33:18] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:18] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:18] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests OK INFO  [2022-05-19 20:33:19] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:19] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests OK INFO  [2022-05-19 20:33:19] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:19] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests OK INFO  [2022-05-19 20:33:19] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:19] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests OK INFO  [2022-05-19 20:33:19] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:19] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests OK INFO  [2022-05-19 20:33:19] ** Raw data from Skyline imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Skyline cleaned successfully.
INFO  [2022-05-19 20:33:19] ** 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 OK 
test_SpectronauttoMSstatsLiPFormat.R    2 tests OK INFO  [2022-05-19 20:33:19] ** Raw data from Spectronaut imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Spectronaut cleaned successfully.
INFO  [2022-05-19 20:33:19] ** Using annotation extracted from quantification data.
INFO  [2022-05-19 20:33:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2022-05-19 20:33:19] ** 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  [2022-05-19 20:33:19] ** PGQvalue not found in input columns.
INFO  [2022-05-19 20:33:19] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2022-05-19 20:33:19] ** Features with all missing measurements across runs are removed.
INFO  [2022-05-19 20:33:19] ** Shared peptides are removed.
INFO  [2022-05-19 20:33:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2022-05-19 20:33:19] ** Features with one or two measurements across runs are removed.
INFO  [2022-05-19 20:33:19] ** Run annotation merged with quantification data.
INFO  [2022-05-19 20:33:19] ** Features with one or two measurements across runs are removed.
INFO  [2022-05-19 20:33:19] ** Fractionation handled.
INFO  [2022-05-19 20:33:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2022-05-19 20:33:19] ** 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  [2022-05-19 20:33:19] ** Raw data from Spectronaut imported successfully.
INFO  [2022-05-19 20:33:19] ** Raw data from Spectronaut cleaned successfully.
INFO  [2022-05-19 20:33:19] ** Using annotation extracted from quantification data.
INFO  [2022-05-19 20:33:19] ** 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 20.6s

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  [2022-05-19 20:33:40]  == Start to test and get inference in whole plot ...

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INFO  [2022-05-19 20:33:41]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2022-05-19 20:33:41]  == Start to test and get inference in whole plot ...

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INFO  [2022-05-19 20:33:41]  == 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 11.3s
All ok, 111 results (37.7s)
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 
 43.869   0.777  44.482 

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

nameusersystemelapsed
LiPRawData0.0130.0040.017
MSstatsLiP_Summarized0.0090.0040.013
MSstatsLiP_data0.0060.0000.005
MSstatsLiP_model0.0070.0000.008
PCAPlotLiP1.8520.0721.924
ResistanceBarcodePlotLiP0.0010.0000.001
SkylineTest0.0050.0000.004
SkylinetoMSstatsLiPFormat0.0000.0030.004
SpectronauttoMSstatsLiPFormat0.2550.0200.235
StructuralBarcodePlotLiP5.2410.0205.262
TrPRawData0.0010.0040.004
annotSite0.0010.0000.001
calculateProteolyticResistance0.0080.0000.008
calculateTrypticity0.0090.0040.014
correlationPlotLiP0.2310.0000.232
dataProcessPlotsLiP20.211 0.17220.384
dataSummarizationLiP0.5350.0080.543
groupComparisonLiP0.4690.0000.469
groupComparisonPlotsLiP1.4800.0681.547
locateMod0.0000.0000.001
locatePTM0.0830.0030.087
raw_lip0.0510.0030.055
raw_prot0.0540.0040.058
tidyFasta0.0290.0000.028
trypticHistogramLiP0.3070.0070.315