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This page was generated on 2024-03-04 11:37:36 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1351/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsShiny 1.4.2  (landing page)
Devon Kohler
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/MSstatsShiny
git_branch: RELEASE_3_18
git_last_commit: ebfa3eb
git_last_commit_date: 2023-12-13 10:17:48 -0500 (Wed, 13 Dec 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MSstatsShiny on lconway


To the developers/maintainers of the MSstatsShiny package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsShiny.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: MSstatsShiny
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsShiny_1.4.2.tar.gz
StartedAt: 2024-03-03 22:03:37 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 22:07:56 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 259.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsShiny.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsShiny_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/MSstatsShiny.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘MSstatsShiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsShiny’ version ‘1.4.2’
* 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 ‘MSstatsShiny’ 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘MSstatsTMT:::.logSum’ ‘MSstatsTMT:::.summarizeSimpleStat’
  ‘MSstatsTMT:::.summarizeTMP’
  ‘MSstatsTMT:::MSstatsFitComparisonModelsTMT’
  ‘MSstatsTMT:::MSstatsGroupComparisonOutputTMT’
  ‘MSstatsTMT:::MSstatsModerateTTest’
  ‘MSstatsTMT:::MSstatsNormalizeTMT’
  ‘MSstatsTMT:::MSstatsPrepareForGroupComparisonTMT’
  ‘MSstatsTMT:::MSstatsPrepareForSummarizationTMT’
  ‘MSstatsTMT:::MSstatsSummarizationOutputTMT’
  ‘MSstatsTMT:::MSstatsTestSingleProteinTMT’
  ‘MSstatsTMT:::getProcessedTMT’ ‘MSstatsTMT:::getSummarizedTMT’
  ‘shinyBS:::buildTooltipOrPopoverOptionsList’ ‘shinyBS:::shinyBSDep’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getAnnot: no visible binding for global variable ‘annotation.pd’
getSummary1: no visible binding for global variable ‘Condition’
getSummary1: no visible binding for global variable ‘BioReplicate’
getSummary1: no visible binding for global variable ‘Mixture’
getSummary1: no visible binding for global variable ‘Run’
getSummary1: no visible binding for global variable ‘TechRepMixture’
getSummary1: no visible binding for global variable ‘Fraction’
getSummary1: no visible binding for global variable ‘Condition_Run’
getSummary1: no visible binding for global variable ‘BioReplicate_Run’
getSummary1: no visible binding for global variable ‘Number of
  Fractions’
getSummary2: no visible binding for global variable ‘ProteinName’
getSummary2: no visible binding for global variable ‘PeptideSequence’
getSummary2: no visible binding for global variable ‘Charge’
getSummary2: no visible binding for global variable ‘PrecursorCharge’
getSummary2: no visible binding for global variable ‘FragmentIon’
getSummary2: no visible binding for global variable ‘ProductCharge’
getSummary2: no visible binding for global variable ‘FEATURES’
getSummary2: no visible binding for global variable ‘Intensity’
getSummary2: no visible binding for global variable ‘Min_Intensity’
getSummary2: no visible binding for global variable ‘Max_Intensity’
getSummary2: no visible binding for global variable ‘npep’
getSummary2: no visible binding for global variable ‘nfea’
getSummary2: no visible binding for global variable
  ‘Features_Peptides_min’
getSummary2: no visible binding for global variable
  ‘Features_Peptides_max’
getSummary2: no visible binding for global variable
  ‘Peptides_Proteins_min’
getSummary2: no visible binding for global variable
  ‘Peptides_Proteins_max’
loadpageServer: no visible global function definition for
  ‘moduleServer’
server: no visible global function definition for ‘callModule’
Undefined global functions or variables:
  BioReplicate BioReplicate_Run Charge Condition Condition_Run FEATURES
  Features_Peptides_max Features_Peptides_min Fraction FragmentIon
  Intensity Max_Intensity Min_Intensity Mixture Number of Fractions
  PeptideSequence Peptides_Proteins_max Peptides_Proteins_min
  PrecursorCharge ProductCharge ProteinName Run TechRepMixture
  annotation.pd callModule moduleServer nfea npep
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
tmt_model              7.427  0.186   7.721
apply_adj              5.501  0.131   5.699
tmt_summarization_loop 5.255  0.156   5.493
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.18-bioc/meat/MSstatsShiny.Rcheck/00check.log’
for details.



Installation output

MSstatsShiny.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘MSstatsShiny’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MSstatsShiny)

Tests output

MSstatsShiny.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(mockery)
> library(MSstatsShiny)
> 
> test_check("MSstatsShiny")
Loading required package: shiny
Reached in evidence
Reached in evidence
Reached in evidence
Reached in evidence
Reached in unmod
Reached in unmod
Reached in proteins_group
Reached in proteins_group
Reached in proteins_group
Reached in proteins_group
Reached in maxq_ptm_sites
Reached in maxq_ptm_sites
Reached in ump annot
Reached in ump annot
Reached in ump annot
Reached in ump annot
[1] "Inside Annot"
[1] "before reading annot file"
[1] "after reading annot file"
[1] "Inside Annot"
[1] "Inside Annot"
[1] "before reading annot file"
[1] "after reading annot file"
Reached in maxq annot
Reached in maxq annot
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is  
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
[1] "list"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
[1] "list"
[1] "+++++++++ In getData +++++++++"
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is maxq 
Reached in maxq
INFO  [2024-03-03 22:07:18] ** Raw data from MaxQuant imported successfully.
INFO  [2024-03-03 22:07:18] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-03-03 22:07:19] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-03-03 22:07:19] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-03-03 22:07:19] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-03-03 22:07:19] ** Rows with values of Onlyidentifiedbysite equal to + are removed 
INFO  [2024-03-03 22:07:19] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO  [2024-03-03 22:07:19] ** Raw data from MaxQuant cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using provided annotation.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Fractionation handled.
INFO  [2024-03-03 22:07:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is PD 
INFO  [2024-03-03 22:07:19] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2024-03-03 22:07:19] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using provided annotation.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Fractionation handled.
INFO  [2024-03-03 22:07:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is prog 
Reached in prog
INFO  [2024-03-03 22:07:19] ** Raw data from Progenesis imported successfully.
INFO  [2024-03-03 22:07:19] ** Raw data from Progenesis cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using provided annotation.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:19] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Fractionation handled.
INFO  [2024-03-03 22:07:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sky 
Reached here in skyline
INFO  [2024-03-03 22:07:19] ** Raw data from Skyline imported successfully.
INFO  [2024-03-03 22:07:19] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using annotation extracted from quantification data.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2024-03-03 22:07:19] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN  [2024-03-03 22:07:19] ** DetectionQValue not found in input columns.
INFO  [2024-03-03 22:07:19] ** Sequences containing DECOY, Decoys are removed.
INFO  [2024-03-03 22:07:19] ** Three isotopic preaks per feature and run are summed
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:19] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Fractionation handled.
INFO  [2024-03-03 22:07:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sky 
Reached here in skyline
INFO  [2024-03-03 22:07:19] ** Raw data from Skyline imported successfully.
INFO  [2024-03-03 22:07:19] ** Raw data from Skyline cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using annotation extracted from quantification data.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Rows with values of StandardType equal to iRT are removed 
INFO  [2024-03-03 22:07:19] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN  [2024-03-03 22:07:19] ** DetectionQValue not found in input columns.
INFO  [2024-03-03 22:07:19] ** Sequences containing DECOY, Decoys are removed.
INFO  [2024-03-03 22:07:19] ** Three isotopic preaks per feature and run are summed
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:19] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Fractionation handled.
INFO  [2024-03-03 22:07:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is openms 
INFO  [2024-03-03 22:07:19] ** Raw data from OpenMS imported successfully.
INFO  [2024-03-03 22:07:19] ** Raw data from OpenMS cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using annotation extracted from quantification data.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:19] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Fractionation handled.
INFO  [2024-03-03 22:07:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is ump 
INFO  [2024-03-03 22:07:19] ** Raw data from DIAUmpire imported successfully.
INFO  [2024-03-03 22:07:19] ** Using selected fragments.
INFO  [2024-03-03 22:07:19] ** Extracted the data from selected fragments and/or peptides.
INFO  [2024-03-03 22:07:19] ** Raw data from DIAUmpire cleaned successfully.
INFO  [2024-03-03 22:07:19] ** Using provided annotation.
INFO  [2024-03-03 22:07:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:19] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, FragmentIon
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:19] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:19] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:19] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:20] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:20] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:20] ** Fractionation handled.
INFO  [2024-03-03 22:07:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:20] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
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File type is spec 
INFO  [2024-03-03 22:07:20] ** Raw data from Spectronaut imported successfully.
INFO  [2024-03-03 22:07:20] ** Raw data from Spectronaut cleaned successfully.
INFO  [2024-03-03 22:07:20] ** Using annotation extracted from quantification data.
INFO  [2024-03-03 22:07:20] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:20] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:20] ** Intensities with values not smaller than 0.01 in PGQvalue are replaced with NA
INFO  [2024-03-03 22:07:20] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO  [2024-03-03 22:07:20] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:20] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:20] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:20] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:20] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:20] ** Fractionation handled.
INFO  [2024-03-03 22:07:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:20] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
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File type is open 
INFO  [2024-03-03 22:07:20] ** Raw data from OpenSWATH imported successfully.
INFO  [2024-03-03 22:07:20] ** Raw data from OpenSWATH cleaned successfully.
INFO  [2024-03-03 22:07:20] ** Using provided annotation.
INFO  [2024-03-03 22:07:20] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:20] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon
  - Shared peptides will be removed.
  - Proteins with a single feature will be removed.
  - Features with less than 3 measurements across runs will be removed.
INFO  [2024-03-03 22:07:20] ** Rows with values of decoy equal to 1 are removed 
INFO  [2024-03-03 22:07:20] ** Rows with values not smaller than 0.01 in m_score are removed 
INFO  [2024-03-03 22:07:20] ** Features with all missing measurements across runs are removed.
INFO  [2024-03-03 22:07:20] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:20] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:20] Proteins with a single feature are removed.
INFO  [2024-03-03 22:07:20] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:20] ** Fractionation handled.
INFO  [2024-03-03 22:07:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:20] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
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File type is maxq 
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INFO  [2024-03-03 22:07:20] ** Raw data from MaxQuant imported successfully.
INFO  [2024-03-03 22:07:20] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-03-03 22:07:20] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-03-03 22:07:20] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2024-03-03 22:07:20] ** Rows with values of Reverse equal to + are removed 
INFO  [2024-03-03 22:07:20] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2024-03-03 22:07:20] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** Raw data from MaxQuant cleaned successfully.
INFO  [2024-03-03 22:07:20] ** Using provided annotation.
INFO  [2024-03-03 22:07:20] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:20] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2024-03-03 22:07:20] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** PSMs have been aggregated to peptide ions.
INFO  [2024-03-03 22:07:20] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** Fractionation handled.
INFO  [2024-03-03 22:07:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:20] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
 [1] "ProteinName"     "PeptideSequence" "Charge"          "PSM"            
 [5] "Mixture"         "TechRepMixture"  "Run"             "Channel"        
 [9] "BioReplicate"    "Condition"       "Intensity"      
[1] "+++++++++ In getData +++++++++"
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File type is openms 
INFO  [2024-03-03 22:07:20] ** Raw data from OpenMS imported successfully.
INFO  [2024-03-03 22:07:20] ** Raw data from OpenMS cleaned successfully.
INFO  [2024-03-03 22:07:20] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2024-03-03 22:07:20] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** PSMs have been aggregated to peptide ions.
INFO  [2024-03-03 22:07:20] ** For peptides overlapped between fractions of 2_2_2 use the fraction with maximal average abundance.
INFO  [2024-03-03 22:07:20] ** For peptides overlapped between fractions of 3_3_3 use the fraction with maximal average abundance.
INFO  [2024-03-03 22:07:20] ** Fractions belonging to same mixture have been combined.
INFO  [2024-03-03 22:07:20] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:20] ** Fractionation handled.
INFO  [2024-03-03 22:07:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:20] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
 [1] "ProteinName"     "PeptideSequence" "Charge"          "PSM"            
 [5] "Mixture"         "TechRepMixture"  "Run"             "Channel"        
 [9] "BioReplicate"    "Condition"       "Intensity"      
[1] "+++++++++ In getData +++++++++"
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File type is spmin 
INFO  [2024-03-03 22:07:21] ** Raw data from SpectroMine imported successfully.
INFO  [2024-03-03 22:07:21] ** Raw data from SpectroMine cleaned successfully.
INFO  [2024-03-03 22:07:21] ** Using provided annotation.
INFO  [2024-03-03 22:07:21] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2024-03-03 22:07:21] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2024-03-03 22:07:21] ** Intensities with values not smaller than 0.01 in PGQValue are replaced with NA
INFO  [2024-03-03 22:07:21] ** Intensities with values not smaller than 0.01 in Qvalue are replaced with NA
INFO  [2024-03-03 22:07:21] ** Features with all missing measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:21] ** Shared peptides are removed.
INFO  [2024-03-03 22:07:21] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:21] ** PSMs have been aggregated to peptide ions.
INFO  [2024-03-03 22:07:21] ** Run annotation merged with quantification data.
INFO  [2024-03-03 22:07:21] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO  [2024-03-03 22:07:21] ** Fractions belonging to same mixture have been combined.
INFO  [2024-03-03 22:07:21] ** Features with one or two measurements across channels within each run are removed.
INFO  [2024-03-03 22:07:21] ** Fractionation handled.
INFO  [2024-03-03 22:07:21] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:21] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
Reached here in skyline
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[1] "+++++++++ In getSummary1 +++++++++"
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[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In getSummary1 +++++++++"
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[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In getSummary1 +++++++++"
[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In getSummary2 +++++++++"
[1] "+++++++++ In getData +++++++++"
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File type is sample 
 [1] "Number of PTMs"             "Number of PTM Features"    
 [3] "Number of Features/PTM"     "PTM Intensity Range"       
 [5] "Number of Unmod Proteins"   "Number of Protein Peptides"
 [7] "Number of Protein Features" "Number of Features/Peptide"
 [9] "Number of Peptides/Protein" "Protein Intensity Range"   
[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In getSummary2 +++++++++"
[1] "+++++++++ In getData +++++++++"
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File type is sample 
 [1] "Number of PTMs"             "Number of PTM Features"    
 [3] "Number of Features/PTM"     "PTM Intensity Range"       
 [5] "Number of Unmod Proteins"   "Number of Protein Peptides"
 [7] "Number of Protein Features" "Number of Features/Peptide"
 [9] "Number of Peptides/Protein" "Protein Intensity Range"   
[1] "+++++++++ In getData +++++++++"
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File type is sample 
[1] "+++++++++ In getSummary2 +++++++++"
[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
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File type is sample 
INFO  [2024-03-03 22:07:22] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:22] ** Fractionation handled.
INFO  [2024-03-03 22:07:22] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:22] ** Use all features that the dataset originally has.
INFO  [2024-03-03 22:07:23] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:23] ** Fractionation handled.
INFO  [2024-03-03 22:07:23] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:23] ** Use all features that the dataset originally has.
[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
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INFO  [2024-03-03 22:07:24] ** MSstatsTMT - proteinSummarization function
INFO  [2024-03-03 22:07:24] ** Use all features that the dataset originally has.
INFO  [2024-03-03 22:07:24] ** Use all features that the dataset originally has.
INFO  [2024-03-03 22:07:25] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
INFO  [2024-03-03 22:07:25] ** MSstatsTMT - proteinSummarization function
INFO  [2024-03-03 22:07:25] ** Use all features that the dataset originally has.
INFO  [2024-03-03 22:07:26] ** Use all features that the dataset originally has.
INFO  [2024-03-03 22:07:29] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
[1] "+++++++++ In getData +++++++++"
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[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
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INFO  [2024-03-03 22:07:29] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:29] ** Fractionation handled.
INFO  [2024-03-03 22:07:29] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:29] ** Use all features that the dataset originally has.
[1] "+++++++++ In Data Comparison +++++++++"
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
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INFO  [2024-03-03 22:07:29] ** MSstatsTMT - proteinSummarization function
INFO  [2024-03-03 22:07:29] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
INFO  [2024-03-03 22:07:29] ** MSstatsTMT - proteinSummarization function
INFO  [2024-03-03 22:07:30] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
INFO  [2024-03-03 22:07:30] Design: 2 mixtures.
INFO  [2024-03-03 22:07:30] Design: 1 MS run per mixture.
INFO  [2024-03-03 22:07:30] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-03-03 22:07:30] Model fitting for 90 proteins.

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INFO  [2024-03-03 22:07:32] Design: 2 mixtures.
INFO  [2024-03-03 22:07:32] Design: 1 MS run per mixture.
INFO  [2024-03-03 22:07:32] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2024-03-03 22:07:32] Model fitting for 85 proteins.

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[1] "+++++++++ In Data Comparison +++++++++"
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
INFO  [2024-03-03 22:07:39] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:39] ** Fractionation handled.
INFO  [2024-03-03 22:07:39] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:39] ** Use all features that the dataset originally has.
INFO  [2024-03-03 22:07:40] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:40] ** Fractionation handled.
INFO  [2024-03-03 22:07:40] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:40] ** Use all features that the dataset originally has.

  |                                                                            
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  |                                                                      |   0%[1] "+++++++++ In Data Comparison +++++++++"
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample 
INFO  [2024-03-03 22:07:45] ** Features with one or two measurements across runs are removed.
INFO  [2024-03-03 22:07:45] ** Fractionation handled.
INFO  [2024-03-03 22:07:45] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2024-03-03 22:07:45] ** Use all features that the dataset originally has.

  |                                                                            
  |                                                                      |   0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 114 ]
> 
> proc.time()
   user  system elapsed 
 34.992   1.403  36.880 

Example timings

MSstatsShiny.Rcheck/MSstatsShiny-Ex.timings

nameusersystemelapsed
QC_check0.0010.0010.001
annotation.mine0.0070.0030.010
annotation.mq0.0030.0020.005
annotation.pd0.0030.0010.005
apply_adj5.5010.1315.699
dia_skyline_model0.0490.0620.113
dia_skyline_summarized0.5461.3222.053
evidence0.0600.0230.085
example_dia_skyline0.2330.0100.245
example_skyline_annotation0.0030.0020.005
groupComparisonPlots20.4000.0120.418
launch_MSstatsShiny000
lf_model0.2500.0060.258
lf_summarization_loop3.8210.9214.793
proteinGroups0.2540.0430.299
radioTooltip0.0050.0000.006
raw.mine0.1390.0040.144
raw.om0.0500.0020.052
raw.pd0.0610.0050.066
tmt_model7.4270.1867.721
tmt_pd_model0.1020.0100.116
tmt_pd_summarized0.7811.5142.648
tmt_summarization_loop5.2550.1565.493
uiObject000
xy_str0.0000.0000.001