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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1316/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsLiP 1.6.0  (landing page)
Devon Kohler
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MSstatsLiP
git_branch: RELEASE_3_17
git_last_commit: c868f6d
git_last_commit_date: 2023-04-25 11:33:53 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MSstatsLiP on kjohnson2


To the developers/maintainers of the MSstatsLiP package:
- 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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2023-10-18 10:03:58 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 10:10:16 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 378.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsLiP.Rcheck
Warnings: 0

Command output

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###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsLiP.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsLiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLiP’ version ‘1.6.0’
* 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: ‘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      29.357  0.391  45.290
StructuralBarcodePlotLiP  3.908  0.060   5.344
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsLiP.Rcheck/00check.log’
for details.



Installation output

MSstatsLiP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsLiP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c model_adjustment.cpp -o model_adjustment.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.

test_SkylinetoMSstatsLiPFormat.R    3 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    4 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    5 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    6 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    7 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    8 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R    9 tests OK INFO  [2023-10-18 10:08:48] ** Raw data from Skyline imported successfully.
INFO  [2023-10-18 10:08:48] ** Raw data from Skyline cleaned successfully.
INFO  [2023-10-18 10:08:48] ** Using annotation extracted from quantification data.

test_SkylinetoMSstatsLiPFormat.R   10 tests OK 0.7s

test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    0 tests    
test_SpectronauttoMSstatsLiPFormat.R    1 tests OK 
test_SpectronauttoMSstatsLiPFormat.R    2 tests OK INFO  [2023-10-18 10:08:49] ** Raw data from Spectronaut imported successfully.
INFO  [2023-10-18 10:08:49] ** Raw data from Spectronaut cleaned successfully.
INFO  [2023-10-18 10:08:49] ** Using annotation extracted from quantification data.
INFO  [2023-10-18 10:08:49] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-10-18 10:08:49] ** 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  [2023-10-18 10:08:49] ** PGQvalue not found in input columns.
INFO  [2023-10-18 10:08:49] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2023-10-18 10:08:49] ** Features with all missing measurements across runs are removed.
INFO  [2023-10-18 10:08:49] ** Shared peptides are removed.
INFO  [2023-10-18 10:08:49] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2023-10-18 10:08:49] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:08:49] ** Run annotation merged with quantification data.
INFO  [2023-10-18 10:08:49] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:08:49] ** Fractionation handled.
INFO  [2023-10-18 10:08:49] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2023-10-18 10:08:49] ** 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  [2023-10-18 10:08:49] ** Raw data from Spectronaut imported successfully.
INFO  [2023-10-18 10:08:49] ** Raw data from Spectronaut cleaned successfully.
INFO  [2023-10-18 10:08:49] ** Using annotation extracted from quantification data.
INFO  [2023-10-18 10:08:49] ** 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 1.3s

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 44.3s

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 0.3s

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  [2023-10-18 10:09:35]  == Start to test and get inference in whole plot ...

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INFO  [2023-10-18 10:09:35]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2023-10-18 10:09:35]  == Start to test and get inference in whole plot ...

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INFO  [2023-10-18 10:09:35]  == 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 1.0s

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 8.8s

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 16.3s
All ok, 111 results (1m 12.7s)
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 
 53.573   1.118  83.694 

Example timings

MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings

nameusersystemelapsed
LiPRawData0.0170.0020.026
MSstatsLiP_Summarized0.0130.0020.020
MSstatsLiP_data0.0050.0010.008
MSstatsLiP_model0.0070.0020.013
PCAPlotLiP1.9280.0672.904
ResistanceBarcodePlotLiP0.0010.0010.004
SkylineTest0.0040.0010.008
SkylinetoMSstatsLiPFormat0.0040.0010.008
SpectronauttoMSstatsLiPFormat0.3050.0130.430
StructuralBarcodePlotLiP3.9080.0605.344
TrPRawData0.0030.0010.006
annotSite0.0010.0000.001
calculateProteolyticResistance0.0090.0010.011
calculateTrypticity0.0150.0020.021
correlationPlotLiP0.3830.0080.498
dataProcessPlotsLiP29.357 0.39145.290
dataSummarizationLiP0.7440.0201.188
groupComparisonLiP0.4990.0100.779
groupComparisonPlotsLiP2.2670.0373.534
locateMod0.0000.0000.001
locatePTM0.1370.0040.221
raw_lip0.0820.0020.128
raw_prot0.0930.0020.146
tidyFasta0.0350.0020.067
trypticHistogramLiP0.3770.0060.590