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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 1318/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 2.2.4  (landing page)
Devon Kohler
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MSstatsPTM
git_branch: RELEASE_3_17
git_last_commit: 356a049
git_last_commit_date: 2023-06-27 10:52:29 -0400 (Tue, 27 Jun 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MSstatsPTM on kjohnson2


To the developers/maintainers of the MSstatsPTM 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: MSstatsPTM
Version: 2.2.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.2.4.tar.gz
StartedAt: 2023-10-18 10:07:27 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 10:13:12 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 345.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsPTM.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 ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.2.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsPTM’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘MSstats:::.getMedianSigmaSubject’ ‘MSstats:::.getVarComponent’
  ‘MSstatsConvert:::.filterFewMeasurements’
  ‘MSstatsConvert:::.filterManyColumns’
  ‘MSstatsConvert:::.getChannelColumns’
  ‘MSstatsConvert:::.standardizeColnames’
  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
.format.data.process.plots: no visible binding for global variable
  ‘ABUNDANCE’
.pivotPS: no visible binding for global variable ‘..keep_cols’
.plot.model.volcano: no visible binding for global variable
  ‘text.angle’
.progensis.add.sites: no visible binding for global variable
  ‘..col_order’
.qc.all.plot.lf: no visible binding for global variable ‘text.angle’
.qc.single.plot.lf: no visible binding for global variable ‘text.angle’
.removeCutoffSites: no visible binding for global variable
  ‘..mod_pep_col’
.rmConfounded: no visible binding for global variable ‘..col_res’
MSstatsPTMSiteLocator: no visible binding for global variable
  ‘..mod_pep_col’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘TMT.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘ptm.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘mod.num’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘which.proteinid.ptm’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
  ‘PeptideSequence’
PStoMSstatsPTMFormat: no visible binding for global variable
  ‘Intensity’
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
  ‘Type’
SkylinetoMSstatsPTMFormat: no visible binding for global variable
  ‘annotation_prot’
dataProcessPlotsPTM: no visible binding for global variable
  ‘PROTEINNAME’
dataProcessPlotsPTM: no visible binding for global variable
  ‘GLOBALPROTEIN’
dataSummarizationPTM: no visible binding for global variable ‘address’
locatePTM: no visible binding for global variable ‘..col_seq’
locatePTM: no visible binding for global variable ‘..col_fasta’
Undefined global functions or variables:
  ..col_fasta ..col_order ..col_res ..col_seq ..keep_cols ..mod_pep_col
  ABUNDANCE GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence
  TMT.keyword Type address annotation_prot mod.num ptm.keyword
  text.angle which.proteinid.ptm
* 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
groupComparisonPlotsPTM  15.348  0.216  23.300
designSampleSizePTM       5.692  0.095   8.520
groupComparisonPTM        4.967  0.090   7.532
dataSummarizationPTM_TMT  4.897  0.108   7.595
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MSstatsPTM.Rcheck/00check.log’
for details.



Installation output

MSstatsPTM.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘MSstatsPTM’ ...
** 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 MSstatsPTM.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-MSstatsPTM/00new/MSstatsPTM/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 (MSstatsPTM)

Tests output

MSstatsPTM.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("MSstatsPTM")
+ }

test_converters.R.............    0 tests    
test_converters.R.............    0 tests    
test_converters.R.............    1 tests OK 
test_converters.R.............    2 tests OK 
test_converters.R.............    3 tests OK 
test_converters.R.............    4 tests OK 
test_converters.R.............    5 tests OK 
test_converters.R.............    5 tests OK 
test_converters.R.............    5 tests OK 
test_converters.R.............    6 tests OK 
test_converters.R.............    7 tests OK 
test_converters.R.............    8 tests OK 
test_converters.R.............    9 tests OK 
test_converters.R.............   10 tests OK 
test_converters.R.............   10 tests OK 
test_converters.R.............   10 tests OK 
test_converters.R.............   11 tests OK 
test_converters.R.............   12 tests OK 
test_converters.R.............   13 tests OK 
test_converters.R.............   14 tests OK 
test_converters.R.............   14 tests OK 
test_converters.R.............   14 tests OK INFO  [2023-10-18 10:12:19] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2023-10-18 10:12:19] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2023-10-18 10:12:19] ** Using provided annotation.
INFO  [2023-10-18 10:12:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-10-18 10:12:19] ** 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  [2023-10-18 10:12:19] ** Features with all missing measurements across runs are removed.
INFO  [2023-10-18 10:12:19] ** Shared peptides are removed.
INFO  [2023-10-18 10:12:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2023-10-18 10:12:19] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:12:19] ** Run annotation merged with quantification data.
INFO  [2023-10-18 10:12:19] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:12:19] ** Fractionation handled.
INFO  [2023-10-18 10:12:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2023-10-18 10:12:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   15 tests OK INFO  [2023-10-18 10:12:21] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2023-10-18 10:12:21] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2023-10-18 10:12:21] ** Using provided annotation.
INFO  [2023-10-18 10:12:21] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-10-18 10:12:21] ** 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 across runs will be removed.
INFO  [2023-10-18 10:12:21] ** Features with all missing measurements across runs are removed.
INFO  [2023-10-18 10:12:21] ** Shared peptides are removed.
INFO  [2023-10-18 10:12:21] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2023-10-18 10:12:21] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:12:21] ** Run annotation merged with quantification data.
INFO  [2023-10-18 10:12:21] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:12:21] ** Fractionation handled.
INFO  [2023-10-18 10:12:21] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2023-10-18 10:12:21] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   16 tests OK 
test_converters.R.............   17 tests OK INFO  [2023-10-18 10:12:22] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2023-10-18 10:12:22] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2023-10-18 10:12:22] ** Using provided annotation.
INFO  [2023-10-18 10:12:22] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO  [2023-10-18 10:12:22] ** 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  [2023-10-18 10:12:22] ** Features with all missing measurements across runs are removed.
INFO  [2023-10-18 10:12:22] ** Shared peptides are removed.
INFO  [2023-10-18 10:12:22] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2023-10-18 10:12:22] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:12:22] ** Run annotation merged with quantification data.
INFO  [2023-10-18 10:12:22] ** Features with one or two measurements across runs are removed.
INFO  [2023-10-18 10:12:22] ** Fractionation handled.
INFO  [2023-10-18 10:12:22] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO  [2023-10-18 10:12:22] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.

test_converters.R.............   18 tests OK 
test_converters.R.............   19 tests OK 
test_converters.R.............   20 tests OK 10.2s

test_dataSummarizationPTM.R...    0 tests    
test_dataSummarizationPTM.R...    1 tests OK 
test_dataSummarizationPTM.R...    2 tests OK 
test_dataSummarizationPTM.R...    3 tests OK 
test_dataSummarizationPTM.R...    4 tests OK 
test_dataSummarizationPTM.R...    5 tests OK 
test_dataSummarizationPTM.R...    6 tests OK 
test_dataSummarizationPTM.R...    7 tests OK 
test_dataSummarizationPTM.R...    8 tests OK 
test_dataSummarizationPTM.R...    9 tests OK 
test_dataSummarizationPTM.R...   10 tests OK 
test_dataSummarizationPTM.R...   11 tests OK 
test_dataSummarizationPTM.R...   12 tests OK 
test_dataSummarizationPTM.R...   13 tests OK 
test_dataSummarizationPTM.R...   14 tests OK 
test_dataSummarizationPTM.R...   15 tests OK 
test_dataSummarizationPTM.R...   16 tests OK 
test_dataSummarizationPTM.R...   17 tests OK 
test_dataSummarizationPTM.R...   18 tests OK 
test_dataSummarizationPTM.R...   19 tests OK 
test_dataSummarizationPTM.R...   20 tests OK 
test_dataSummarizationPTM.R...   21 tests OK 
test_dataSummarizationPTM.R...   22 tests OK 
test_dataSummarizationPTM.R...   23 tests OK 
test_dataSummarizationPTM.R...   24 tests OK 
test_dataSummarizationPTM.R...   25 tests OK 
test_dataSummarizationPTM.R...   26 tests OK 
test_dataSummarizationPTM.R...   27 tests OK 
test_dataSummarizationPTM.R...   28 tests OK 
test_dataSummarizationPTM.R...   29 tests OK 
test_dataSummarizationPTM.R...   30 tests OK Starting PTM summarization...

test_dataSummarizationPTM.R...   31 tests OK 0.4s

test_dataSummarizationPTM_TMT.R    0 tests    
test_dataSummarizationPTM_TMT.R    1 tests OK 
test_dataSummarizationPTM_TMT.R    2 tests OK 
test_dataSummarizationPTM_TMT.R    3 tests OK 
test_dataSummarizationPTM_TMT.R    4 tests OK 
test_dataSummarizationPTM_TMT.R    5 tests OK 
test_dataSummarizationPTM_TMT.R    6 tests OK 
test_dataSummarizationPTM_TMT.R    7 tests OK 
test_dataSummarizationPTM_TMT.R    8 tests OK 
test_dataSummarizationPTM_TMT.R    9 tests OK 
test_dataSummarizationPTM_TMT.R   10 tests OK 
test_dataSummarizationPTM_TMT.R   11 tests OK 
test_dataSummarizationPTM_TMT.R   12 tests OK 
test_dataSummarizationPTM_TMT.R   13 tests OK 
test_dataSummarizationPTM_TMT.R   14 tests OK 
test_dataSummarizationPTM_TMT.R   15 tests OK 
test_dataSummarizationPTM_TMT.R   16 tests OK 
test_dataSummarizationPTM_TMT.R   17 tests OK 
test_dataSummarizationPTM_TMT.R   18 tests OK 
test_dataSummarizationPTM_TMT.R   19 tests OK 
test_dataSummarizationPTM_TMT.R   20 tests OK 
test_dataSummarizationPTM_TMT.R   21 tests OK 
test_dataSummarizationPTM_TMT.R   22 tests OK 
test_dataSummarizationPTM_TMT.R   23 tests OK 
test_dataSummarizationPTM_TMT.R   24 tests OK 
test_dataSummarizationPTM_TMT.R   25 tests OK 
test_dataSummarizationPTM_TMT.R   26 tests OK 
test_dataSummarizationPTM_TMT.R   27 tests OK 
test_dataSummarizationPTM_TMT.R   28 tests OK 
test_dataSummarizationPTM_TMT.R   29 tests OK 
test_dataSummarizationPTM_TMT.R   30 tests OK 
test_dataSummarizationPTM_TMT.R   31 tests OK 0.4s

test_groupComparisonPTM.R.....    0 tests    
test_groupComparisonPTM.R.....    0 tests    
test_groupComparisonPTM.R.....    1 tests OK 
test_groupComparisonPTM.R.....    2 tests OK Starting PTM modeling...

test_groupComparisonPTM.R.....    3 tests OK Starting PTM modeling...
INFO  [2023-10-18 10:12:31]  == Start to test and get inference in whole plot ...

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INFO  [2023-10-18 10:12:37]  == Comparisons for all proteins are done.
Starting Protein modeling...
INFO  [2023-10-18 10:12:37]  == Start to test and get inference in whole plot ...

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INFO  [2023-10-18 10:12:38]  == Comparisons for all proteins are done.
Starting adjustment...

test_groupComparisonPTM.R.....    3 tests OK 
test_groupComparisonPTM.R.....    4 tests OK 
test_groupComparisonPTM.R.....    5 tests OK 
test_groupComparisonPTM.R.....    6 tests OK 
test_groupComparisonPTM.R.....    7 tests OK 
test_groupComparisonPTM.R.....    8 tests OK 
test_groupComparisonPTM.R.....    9 tests OK 
test_groupComparisonPTM.R.....   10 tests OK Starting PTM modeling...
INFO  [2023-10-18 10:12:39] Design: 2 mixtures.
INFO  [2023-10-18 10:12:39] Design: 1 MS run per mixture.
INFO  [2023-10-18 10:12:39] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2023-10-18 10:12:39] Model fitting for 90 proteins.

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INFO  [2023-10-18 10:12:43] Testing for 90 proteins:

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Starting Protein modeling...
INFO  [2023-10-18 10:12:44] Design: 2 mixtures.
INFO  [2023-10-18 10:12:44] Design: 1 MS run per mixture.
INFO  [2023-10-18 10:12:44] Design: group comparison design (Different conditions contains different biological subjects).
INFO  [2023-10-18 10:12:44] Model fitting for 85 proteins.

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INFO  [2023-10-18 10:12:53] Testing for 85 proteins:

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Starting adjustment...

test_groupComparisonPTM.R.....   10 tests OK 
test_groupComparisonPTM.R.....   11 tests OK 
test_groupComparisonPTM.R.....   12 tests OK 
test_groupComparisonPTM.R.....   13 tests OK 
test_groupComparisonPTM.R.....   14 tests OK 
test_groupComparisonPTM.R.....   15 tests OK 
test_groupComparisonPTM.R.....   16 tests OK 
test_groupComparisonPTM.R.....   17 tests OK 31.2s
All ok, 99 results (42.2s)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 33.475   0.967  52.954 

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
FragPipetoMSstatsPTMFormat0.5120.0280.842
MSstatsPTMSiteLocator000
MaxQtoMSstatsPTMFormat0.7910.0301.258
PDtoMSstatsPTMFormat0.8790.0361.372
PStoMSstatsPTMFormat0.0920.0020.141
ProgenesistoMSstatsPTMFormat0.0710.0010.112
SkylinetoMSstatsPTMFormat0.0730.0020.115
SpectronauttoMSstatsPTMFormat0.6960.0191.107
annotSite0.0000.0000.001
dataProcessPlotsPTM2.6100.0573.806
dataSummarizationPTM2.4910.0553.540
dataSummarizationPTM_TMT4.8970.1087.595
designSampleSizePTM5.6920.0958.520
fragpipe_annotation0.0010.0010.003
fragpipe_annotation_protein0.0020.0000.005
fragpipe_input0.0050.0010.010
fragpipe_input_protein0.0050.0010.010
groupComparisonPTM4.9670.0907.532
groupComparisonPlotsPTM15.348 0.21623.300
locateMod0.0010.0000.000
locatePTM0.0150.0010.028
maxq_lf_annotation0.0010.0000.002
maxq_lf_evidence0.0100.0040.025
maxq_tmt_annotation0.0020.0010.006
maxq_tmt_evidence0.0140.0070.032
pd_annotation0.0020.0000.001
pd_psm_input0.0120.0030.025
raw.input0.0780.0010.121
raw.input.tmt0.0050.0010.009
spectronaut_annotation0.0020.0000.003
spectronaut_input0.0050.0010.008
summary.data0.3300.3761.067
summary.data.tmt0.6420.7002.088
tidyFasta0.0080.0010.014