Anthony Wu
| Snapshot Date: 2025-11-02 13:40 -0500 (Sun, 02 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/MSstatsPTM |
| git_branch: devel |
| git_last_commit: c7e1180 |
| git_last_commit_date: 2025-10-29 11:02:42 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-03 11:33 -0500 (Mon, 03 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4775 |
| 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 1380/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 2.13.0 (landing page) Anthony Wu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
|
To the developers/maintainers of the MSstatsPTM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.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. |
| Package: MSstatsPTM |
| Version: 2.13.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstatsPTM_2.13.0.tar.gz |
| StartedAt: 2025-11-03 01:24:53 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 01:29:07 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 254.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstatsPTM.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MSstatsPTM_2.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MSstatsPTM.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.13.0’
* 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 ... 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 loading without being on the library search path ... 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
.extract_pd_mods: no visible binding for global variable
‘..sequence_col’
.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’
.savePlotlyPlotHTML: no visible global function definition for
‘txtProgressBar’
.savePlotlyPlotHTML: no visible global function definition for
‘setTxtProgressBar’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
DIANNtoMSstatsPTMFormat: no visible binding for global variable
‘..protein_id_col’
FragPipetoMSstatsPTMFormat: no visible binding for global variable
‘..msstats_cols’
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’
MetamorpheusToMSstatsPTMFormat: no visible binding for global variable
‘..protein_id_col’
PStoMSstatsPTMFormat: no visible binding for global variable
‘Intensity’
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
‘Type’
ProteinProspectortoMSstatsPTMFormat: no visible binding for global
variable ‘..protein_id_col’
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
..msstats_cols ..protein_id_col ..sequence_col ABUNDANCE
GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence TMT.keyword Type
address annotation_prot mod.num ptm.keyword setTxtProgressBar
text.angle txtProgressBar which.proteinid.ptm zip
Consider adding
importFrom("utils", "setTxtProgressBar", "txtProgressBar", "zip")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'dataProcessPTM.Rd'
‘use_log_file’ ‘append’ ‘verbose’ ‘log_file_path’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... INFO
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 13.419 0.123 13.538
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘MSstatsPTM’ ... ** this is package ‘MSstatsPTM’ version ‘2.13.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-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)
MSstatsPTM.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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............. 0 tests
test_converters.R............. 0 tests
test_converters.R............. 0 tests
test_converters.R............. 1 tests [0;32mOK[0m
test_converters.R............. 2 tests [0;32mOK[0m
test_converters.R............. 3 tests [0;32mOK[0m
test_converters.R............. 4 tests [0;32mOK[0m
test_converters.R............. 5 tests [0;32mOK[0m INFO [2025-11-03 01:27:40] ** Raw data from MaxQuant imported successfully.
INFO [2025-11-03 01:27:40] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-11-03 01:27:40] ** Rows with values of Reverse equal to + are removed
INFO [2025-11-03 01:27:40] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** Using provided annotation.
INFO [2025-11-03 01:27:40] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:40] ** 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 kept.
INFO [2025-11-03 01:27:40] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** Shared peptides are removed.
INFO [2025-11-03 01:27:40] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:40] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:40] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** Fractionation handled.
INFO [2025-11-03 01:27:40] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:40] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 5 tests [0;32mOK[0m
test_converters.R............. 7 tests [0;32mOK[0m
test_converters.R............. 8 tests [0;32mOK[0m
test_converters.R............. 9 tests [0;32mOK[0m
test_converters.R............. 10 tests [0;32mOK[0m
test_converters.R............. 11 tests [0;32mOK[0m
test_converters.R............. 12 tests [0;32mOK[0m INFO [2025-11-03 01:27:40] ** Raw data from MaxQuant imported successfully.
INFO [2025-11-03 01:27:40] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-11-03 01:27:40] ** Rows with values of Reverse equal to + are removed
INFO [2025-11-03 01:27:40] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** Using provided annotation.
INFO [2025-11-03 01:27:40] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:40] ** 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 kept.
INFO [2025-11-03 01:27:40] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** Shared peptides are removed.
INFO [2025-11-03 01:27:40] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:40] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:40] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:40] ** Fractionation handled.
INFO [2025-11-03 01:27:40] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:40] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 12 tests [0;32mOK[0m
test_converters.R............. 14 tests [0;32mOK[0m
test_converters.R............. 15 tests [0;32mOK[0m
test_converters.R............. 16 tests [0;32mOK[0m
test_converters.R............. 17 tests [0;32mOK[0m
test_converters.R............. 17 tests [0;32mOK[0m
test_converters.R............. 17 tests [0;32mOK[0m
test_converters.R............. 18 tests [0;32mOK[0m
test_converters.R............. 19 tests [0;32mOK[0m
test_converters.R............. 20 tests [0;32mOK[0m
test_converters.R............. 21 tests [0;32mOK[0m
test_converters.R............. 22 tests [0;32mOK[0m INFO [2025-11-03 01:27:40] ** Raw data from MaxQuant imported successfully.
INFO [2025-11-03 01:27:40] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-11-03 01:27:40] ** Rows with values of Reverse equal to + are removed
INFO [2025-11-03 01:27:40] ** Using provided annotation.
INFO [2025-11-03 01:27:40] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:40] ** 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 [2025-11-03 01:27:40] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:40] ** Shared peptides are removed.
INFO [2025-11-03 01:27:40] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:40] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:40] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:40] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:40] ** Fractionation handled.
INFO [2025-11-03 01:27:40] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:40] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 22 tests [0;32mOK[0m
test_converters.R............. 24 tests [0;32mOK[0m
test_converters.R............. 25 tests [0;32mOK[0m
test_converters.R............. 26 tests [0;32mOK[0m
test_converters.R............. 27 tests [0;32mOK[0m
test_converters.R............. 28 tests [0;32mOK[0m
test_converters.R............. 29 tests [0;32mOK[0m INFO [2025-11-03 01:27:40] ** Raw data from MaxQuant imported successfully.
INFO [2025-11-03 01:27:40] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-11-03 01:27:40] ** Rows with values of Reverse equal to + are removed
INFO [2025-11-03 01:27:40] ** Using provided annotation.
INFO [2025-11-03 01:27:40] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:40] ** 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 [2025-11-03 01:27:40] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:40] ** Shared peptides are removed.
INFO [2025-11-03 01:27:40] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:40] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:40] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:40] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:40] ** Fractionation handled.
INFO [2025-11-03 01:27:41] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:41] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 29 tests [0;32mOK[0m
test_converters.R............. 31 tests [0;32mOK[0m
test_converters.R............. 32 tests [0;32mOK[0m
test_converters.R............. 33 tests [0;32mOK[0m
test_converters.R............. 34 tests [0;32mOK[0m
test_converters.R............. 34 tests [0;32mOK[0m
test_converters.R............. 34 tests [0;32mOK[0m
test_converters.R............. 35 tests [0;32mOK[0m
test_converters.R............. 36 tests [0;32mOK[0m
test_converters.R............. 37 tests [0;32mOK[0m
test_converters.R............. 38 tests [0;32mOK[0m INFO [2025-11-03 01:27:43] ** Raw data from Spectronaut imported successfully.
INFO [2025-11-03 01:27:43] ** Raw data from Spectronaut cleaned successfully.
INFO [2025-11-03 01:27:43] ** Using provided annotation.
INFO [2025-11-03 01:27:43] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:43] ** 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.
INFO [2025-11-03 01:27:43] ** Intensities with values of FExcludedFromQuantification equal to TRUE are replaced with NA
WARN [2025-11-03 01:27:43] ** PGQvalue not found in input columns.
WARN [2025-11-03 01:27:43] ** EGQvalue not found in input columns.
INFO [2025-11-03 01:27:43] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:43] ** Shared peptides are removed.
INFO [2025-11-03 01:27:43] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:43] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:43] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:43] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:43] ** Fractionation handled.
INFO [2025-11-03 01:27:43] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:43] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 38 tests [0;32mOK[0m
test_converters.R............. 40 tests [0;32mOK[0m
test_converters.R............. 41 tests [0;32mOK[0m
test_converters.R............. 42 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 44 tests [0;32mOK[0m
test_converters.R............. 45 tests [0;32mOK[0m
test_converters.R............. 45 tests [0;32mOK[0m
test_converters.R............. 45 tests [0;32mOK[0m
test_converters.R............. 45 tests [0;32mOK[0m INFO [2025-11-03 01:27:44] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:44] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:44] ** Using provided annotation.
INFO [2025-11-03 01:27:44] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:44] ** 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 [2025-11-03 01:27:44] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:44] ** Shared peptides are removed.
INFO [2025-11-03 01:27:44] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:44] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:44] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:44] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:44] ** Fractionation handled.
INFO [2025-11-03 01:27:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:44] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 46 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2025-11-03 01:27:44] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:44] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:44] ** Using provided annotation.
INFO [2025-11-03 01:27:44] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:44] ** 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 [2025-11-03 01:27:44] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:44] ** Shared peptides are removed.
INFO [2025-11-03 01:27:44] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:44] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:44] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:44] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:44] ** Fractionation handled.
INFO [2025-11-03 01:27:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:44] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 47 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2025-11-03 01:27:45] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:45] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:45] ** Using provided annotation.
INFO [2025-11-03 01:27:45] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:45] ** 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 [2025-11-03 01:27:45] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:45] ** Shared peptides are removed.
INFO [2025-11-03 01:27:45] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:45] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:45] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:45] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:45] ** Fractionation handled.
INFO [2025-11-03 01:27:45] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:45] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 48 tests [0;32mOK[0m INFO [2025-11-03 01:27:46] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:46] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:46] ** Using provided annotation.
INFO [2025-11-03 01:27:46] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:46] ** 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 [2025-11-03 01:27:46] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:46] ** Shared peptides are removed.
INFO [2025-11-03 01:27:46] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:46] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:46] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:46] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:46] ** Fractionation handled.
INFO [2025-11-03 01:27:46] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:46] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 49 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m INFO [2025-11-03 01:27:47] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:47] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:47] ** Using provided annotation.
INFO [2025-11-03 01:27:47] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:47] ** 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 [2025-11-03 01:27:47] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:47] ** Shared peptides are removed.
INFO [2025-11-03 01:27:47] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:47] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:47] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:47] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:47] ** Fractionation handled.
INFO [2025-11-03 01:27:47] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:47] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 51 tests [0;32mOK[0m
test_converters.R............. 52 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 53 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2025-11-03 01:27:47] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:47] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:47] ** Using provided annotation.
INFO [2025-11-03 01:27:47] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:47] ** 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 [2025-11-03 01:27:47] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:47] ** Shared peptides are removed.
INFO [2025-11-03 01:27:47] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:47] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:47] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:47] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:47] ** Fractionation handled.
INFO [2025-11-03 01:27:47] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:47] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-11-03 01:27:47] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-11-03 01:27:47] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-11-03 01:27:47] ** Using provided annotation.
INFO [2025-11-03 01:27:47] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:47] ** 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 [2025-11-03 01:27:47] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:47] ** Shared peptides are removed.
INFO [2025-11-03 01:27:47] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:47] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:47] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:47] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO [2025-11-03 01:27:47] ** Fractions belonging to same mixture have been combined.
INFO [2025-11-03 01:27:47] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:47] ** Fractionation handled.
INFO [2025-11-03 01:27:47] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:47] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 53 tests [0;32mOK[0m
test_converters.R............. 55 tests [0;32mOK[0m
test_converters.R............. 56 tests [0;32mOK[0m
test_converters.R............. 57 tests [0;32mOK[0m
test_converters.R............. 58 tests [0;32mOK[0m
test_converters.R............. 59 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 60 tests [0;32mOK[0m
test_converters.R............. 61 tests [0;32mOK[0m
test_converters.R............. 62 tests [0;32mOK[0m
test_converters.R............. 63 tests [0;32mOK[0m
test_converters.R............. 64 tests [0;32mOK[0m
test_converters.R............. 65 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus imported successfully.
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-11-03 01:27:48] ** Using provided annotation.
INFO [2025-11-03 01:27:48] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:48] ** 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 [2025-11-03 01:27:48] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Shared peptides are removed.
INFO [2025-11-03 01:27:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Fractionation handled.
INFO [2025-11-03 01:27:48] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:48] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus imported successfully.
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-11-03 01:27:48] ** Using provided annotation.
INFO [2025-11-03 01:27:48] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:48] ** 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 [2025-11-03 01:27:48] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Shared peptides are removed.
INFO [2025-11-03 01:27:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Fractionation handled.
INFO [2025-11-03 01:27:48] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:48] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 65 tests [0;32mOK[0m
test_converters.R............. 67 tests [0;32mOK[0m
test_converters.R............. 68 tests [0;32mOK[0m
test_converters.R............. 69 tests [0;32mOK[0m
test_converters.R............. 70 tests [0;32mOK[0m
test_converters.R............. 71 tests [0;32mOK[0m
test_converters.R............. 72 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus imported successfully.
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-11-03 01:27:48] ** Using provided annotation.
INFO [2025-11-03 01:27:48] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:48] ** 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 [2025-11-03 01:27:48] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Shared peptides are removed.
INFO [2025-11-03 01:27:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Fractionation handled.
INFO [2025-11-03 01:27:48] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:48] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus imported successfully.
INFO [2025-11-03 01:27:48] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-11-03 01:27:48] ** Using provided annotation.
INFO [2025-11-03 01:27:48] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:48] ** 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 [2025-11-03 01:27:48] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Shared peptides are removed.
INFO [2025-11-03 01:27:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Fractionation handled.
INFO [2025-11-03 01:27:48] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:48] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 72 tests [0;32mOK[0m
test_converters.R............. 74 tests [0;32mOK[0m
test_converters.R............. 75 tests [0;32mOK[0m
test_converters.R............. 76 tests [0;32mOK[0m
test_converters.R............. 77 tests [0;32mOK[0m
test_converters.R............. 78 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 79 tests [0;32mOK[0m
test_converters.R............. 80 tests [0;32mOK[0m
test_converters.R............. 81 tests [0;32mOK[0m INFO [2025-11-03 01:27:48] ** Raw data from Progenesis imported successfully.
INFO [2025-11-03 01:27:48] ** Raw data from Progenesis cleaned successfully.
INFO [2025-11-03 01:27:48] ** Using provided annotation.
INFO [2025-11-03 01:27:48] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:48] ** 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 [2025-11-03 01:27:48] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Shared peptides are removed.
INFO [2025-11-03 01:27:48] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:48] ** Features with one or two measurements across runs are removed.
INFO [2025-11-03 01:27:48] ** Fractionation handled.
INFO [2025-11-03 01:27:48] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:48] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 81 tests [0;32mOK[0m
test_converters.R............. 82 tests [0;32mOK[0m
test_converters.R............. 83 tests [0;32mOK[0m
test_converters.R............. 84 tests [0;32mOK[0m INFO [2025-11-03 01:27:49] ** Raw data from Philosopher imported successfully.
INFO [2025-11-03 01:27:49] ** Using provided annotation.
INFO [2025-11-03 01:27:49] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:49] ** 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 kept.
INFO [2025-11-03 01:27:49] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2025-11-03 01:27:49] ** PeptideProphetProbability not found in input columns.
INFO [2025-11-03 01:27:49] ** Sequences containing Oxidation are removed.
INFO [2025-11-03 01:27:49] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:49] ** Shared peptides are removed.
INFO [2025-11-03 01:27:49] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:49] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:49] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:49] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:49] ** Fractionation handled.
INFO [2025-11-03 01:27:49] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:49] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-11-03 01:27:49] ** Raw data from Philosopher imported successfully.
test_converters.R............. 85 tests [0;32mOK[0m
test_converters.R............. 86 tests [0;32mOK[0m INFO [2025-11-03 01:27:49] ** Raw data from Philosopher imported successfully.
INFO [2025-11-03 01:27:49] ** Using provided annotation.
INFO [2025-11-03 01:27:49] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:49] ** 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 kept.
INFO [2025-11-03 01:27:49] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2025-11-03 01:27:49] ** PeptideProphetProbability not found in input columns.
INFO [2025-11-03 01:27:49] ** Sequences containing Oxidation are removed.
INFO [2025-11-03 01:27:49] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:49] ** Shared peptides are removed.
INFO [2025-11-03 01:27:49] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:49] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:50] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:50] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:50] ** Fractionation handled.
INFO [2025-11-03 01:27:50] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:50] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-11-03 01:27:50] ** Raw data from Philosopher imported successfully.
INFO [2025-11-03 01:27:50] ** Using provided annotation.
INFO [2025-11-03 01:27:50] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:50] ** 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 kept.
INFO [2025-11-03 01:27:50] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2025-11-03 01:27:50] ** PeptideProphetProbability not found in input columns.
INFO [2025-11-03 01:27:50] ** Sequences containing Oxidation are removed.
INFO [2025-11-03 01:27:50] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:50] ** Shared peptides are removed.
INFO [2025-11-03 01:27:50] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:50] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:50] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:50] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:50] ** Fractionation handled.
INFO [2025-11-03 01:27:50] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:50] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 86 tests [0;32mOK[0m
test_converters.R............. 88 tests [0;32mOK[0m
test_converters.R............. 89 tests [0;32mOK[0m
test_converters.R............. 90 tests [0;32mOK[0m
test_converters.R............. 91 tests [0;32mOK[0m
test_converters.R............. 92 tests [0;32mOK[0m
test_converters.R............. 93 tests [0;32mOK[0m
test_converters.R............. 93 tests [0;32mOK[0m
test_converters.R............. 93 tests [0;32mOK[0m
test_converters.R............. 93 tests [0;32mOK[0m
test_converters.R............. 93 tests [0;32mOK[0m
test_converters.R............. 94 tests [0;32mOK[0m
test_converters.R............. 95 tests [0;32mOK[0m INFO [2025-11-03 01:27:50] ** Raw data from FragPipe imported successfully.
INFO [2025-11-03 01:27:50] ** Using annotation extracted from quantification data.
INFO [2025-11-03 01:27:50] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:50] ** 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 kept.
INFO [2025-11-03 01:27:50] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:50] ** Shared peptides are removed.
INFO [2025-11-03 01:27:50] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2025-11-03 01:27:50] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:50] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:50] ** Features with all missing measurements across runs are removed.
INFO [2025-11-03 01:27:50] ** Fractionation handled.
INFO [2025-11-03 01:27:50] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:50] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 95 tests [0;32mOK[0m
test_converters.R............. 96 tests [0;32mOK[0m
test_converters.R............. 97 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 98 tests [0;32mOK[0m
test_converters.R............. 99 tests [0;32mOK[0m
test_converters.R............. 100 tests [0;32mOK[0m
test_converters.R............. 101 tests [0;32mOK[0m
test_converters.R............. 102 tests [0;32mOK[0m
test_converters.R............. 103 tests [0;32mOK[0m INFO [2025-11-03 01:27:51] ** Raw data from ProteinProspector imported successfully.
INFO [2025-11-03 01:27:51] ** Raw data from ProteinProspector cleaned successfully.
INFO [2025-11-03 01:27:51] ** Using provided annotation.
INFO [2025-11-03 01:27:51] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:51] ** 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 [2025-11-03 01:27:51] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:51] ** Shared peptides are removed.
INFO [2025-11-03 01:27:51] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:51] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:51] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:51] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO [2025-11-03 01:27:51] ** Fractions belonging to same mixture have been combined.
INFO [2025-11-03 01:27:51] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:51] ** Fractionation handled.
INFO [2025-11-03 01:27:51] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:51] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-11-03 01:27:51] ** Raw data from ProteinProspector imported successfully.
INFO [2025-11-03 01:27:51] ** Raw data from ProteinProspector cleaned successfully.
INFO [2025-11-03 01:27:51] ** Using provided annotation.
INFO [2025-11-03 01:27:51] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-11-03 01:27:51] ** 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 [2025-11-03 01:27:51] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-11-03 01:27:51] ** Shared peptides are removed.
INFO [2025-11-03 01:27:51] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:51] ** PSMs have been aggregated to peptide ions.
INFO [2025-11-03 01:27:51] ** Run annotation merged with quantification data.
INFO [2025-11-03 01:27:51] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO [2025-11-03 01:27:51] ** Fractions belonging to same mixture have been combined.
INFO [2025-11-03 01:27:51] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-11-03 01:27:51] ** Fractionation handled.
INFO [2025-11-03 01:27:51] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-11-03 01:27:51] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 103 tests [0;32mOK[0m
test_converters.R............. 105 tests [0;32mOK[0m
test_converters.R............. 106 tests [0;32mOK[0m
test_converters.R............. 107 tests [0;32mOK[0m
test_converters.R............. 108 tests [0;32mOK[0m
test_converters.R............. 109 tests [0;32mOK[0m
test_converters.R............. 110 tests [0;32mOK[0m
test_converters.R............. 111 tests [0;32mOK[0m [0;34m12.3s[0m
test_dataSummarizationPTM.R... 0 tests
test_dataSummarizationPTM.R... 1 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 2 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 3 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 4 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 5 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 6 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 7 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 8 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 9 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 10 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 11 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 12 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 13 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 14 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 15 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 16 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 17 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 18 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 19 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 20 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 21 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 22 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 23 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 24 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 25 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 26 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 27 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 28 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 29 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 30 tests [0;32mOK[0m Starting PTM summarization...
test_dataSummarizationPTM.R... 31 tests [0;32mOK[0m [0;34m0.2s[0m
test_dataSummarizationPTM_TMT.R 0 tests
test_dataSummarizationPTM_TMT.R 1 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 2 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 3 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 4 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 5 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 6 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 7 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 8 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 9 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 10 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 11 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 12 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 13 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 14 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 15 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 16 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 17 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 18 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 19 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 20 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 21 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 22 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 23 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 24 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 25 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 26 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 27 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 28 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 29 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 30 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 31 tests [0;32mOK[0m [0;34m0.2s[0m
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 1 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 2 tests [0;32mOK[0m Starting PTM modeling...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m Starting PTM modeling...
INFO [2025-11-03 01:27:55] == Start to test and get inference in whole plot ...
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INFO [2025-11-03 01:27:58] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2025-11-03 01:27:58] == Start to test and get inference in whole plot ...
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INFO [2025-11-03 01:27:59] == Comparisons for all proteins are done.
Starting adjustment...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 4 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 5 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 6 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 7 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 8 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 9 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m Starting PTM modeling...
INFO [2025-11-03 01:28:00] Design: 2 mixtures.
INFO [2025-11-03 01:28:00] Design: 1 MS run per mixture.
INFO [2025-11-03 01:28:00] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2025-11-03 01:28:00] Model fitting for 90 proteins.
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INFO [2025-11-03 01:28:02] Testing for 90 proteins:
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Starting Protein modeling...
INFO [2025-11-03 01:28:02] Design: 2 mixtures.
INFO [2025-11-03 01:28:02] Design: 1 MS run per mixture.
INFO [2025-11-03 01:28:02] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2025-11-03 01:28:02] Model fitting for 85 proteins.
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INFO [2025-11-03 01:28:07] Testing for 85 proteins:
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Starting adjustment...
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 11 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 12 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 13 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 14 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 15 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 16 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 17 tests [0;32mOK[0m [0;34m16.2s[0m
test_utils_checks.R........... 0 tests
test_utils_checks.R........... 1 tests [0;32mOK[0m
test_utils_checks.R........... 2 tests [0;32mOK[0m
test_utils_checks.R........... 2 tests [0;32mOK[0m
test_utils_checks.R........... 3 tests [0;32mOK[0m
test_utils_checks.R........... 3 tests [0;32mOK[0m
test_utils_checks.R........... 4 tests [0;32mOK[0m
test_utils_checks.R........... 4 tests [0;32mOK[0m
test_utils_checks.R........... 5 tests [0;32mOK[0m
test_utils_checks.R........... 5 tests [0;32mOK[0m
test_utils_checks.R........... 6 tests [0;32mOK[0m
test_utils_checks.R........... 6 tests [0;32mOK[0m
test_utils_checks.R........... 7 tests [0;32mOK[0m
test_utils_checks.R........... 7 tests [0;32mOK[0m
test_utils_checks.R........... 8 tests [0;32mOK[0m
test_utils_checks.R........... 8 tests [0;32mOK[0m
test_utils_checks.R........... 9 tests [0;32mOK[0m
test_utils_checks.R........... 9 tests [0;32mOK[0m
test_utils_checks.R........... 10 tests [0;32mOK[0m
test_utils_checks.R........... 11 tests [0;32mOK[0m
test_utils_checks.R........... 11 tests [0;32mOK[0m
test_utils_checks.R........... 12 tests [0;32mOK[0m
test_utils_checks.R........... 13 tests [0;32mOK[0m
test_utils_checks.R........... 13 tests [0;32mOK[0m
test_utils_checks.R........... 14 tests [0;32mOK[0m
test_utils_checks.R........... 14 tests [0;32mOK[0m
test_utils_checks.R........... 15 tests [0;32mOK[0m
test_utils_checks.R........... 16 tests [0;32mOK[0m
test_utils_checks.R........... 16 tests [0;32mOK[0m
test_utils_checks.R........... 17 tests [0;32mOK[0m
test_utils_checks.R........... 18 tests [0;32mOK[0m
test_utils_checks.R........... 18 tests [0;32mOK[0m
test_utils_checks.R........... 19 tests [0;32mOK[0m
test_utils_checks.R........... 20 tests [0;32mOK[0m
test_utils_checks.R........... 21 tests [0;32mOK[0m [0;36m13ms[0m
All ok, 211 results (28.9s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
35.685 0.996 34.818
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsPTMFormat | 0.267 | 0.006 | 0.221 | |
| FragPipetoMSstatsPTMFormat | 1.170 | 0.016 | 1.093 | |
| MSstatsPTMSiteLocator | 0.000 | 0.000 | 0.001 | |
| MaxQtoMSstatsPTMFormat | 0.349 | 0.028 | 0.310 | |
| MetamorpheusToMSstatsPTMFormat | 0.169 | 0.004 | 0.149 | |
| PDtoMSstatsPTMFormat | 1.080 | 0.096 | 1.079 | |
| PStoMSstatsPTMFormat | 0.066 | 0.005 | 0.070 | |
| ProgenesistoMSstatsPTMFormat | 0.072 | 0.010 | 0.069 | |
| ProteinProspectortoMSstatsPTMFormat | 0.355 | 0.084 | 0.388 | |
| SkylinetoMSstatsPTMFormat | 0.047 | 0.007 | 0.054 | |
| SpectronauttoMSstatsPTMFormat | 0.660 | 0.014 | 0.562 | |
| annotSite | 0.000 | 0.001 | 0.001 | |
| dataProcessPlotsPTM | 3.093 | 0.060 | 3.113 | |
| dataSummarizationPTM | 2.345 | 0.046 | 2.202 | |
| dataSummarizationPTM_TMT | 4.334 | 0.107 | 3.868 | |
| designSampleSizePTM | 4.917 | 0.050 | 4.961 | |
| fragpipe_annotation | 0.001 | 0.001 | 0.002 | |
| fragpipe_annotation_protein | 0.002 | 0.000 | 0.001 | |
| fragpipe_input | 0.004 | 0.001 | 0.005 | |
| fragpipe_input_protein | 0.003 | 0.002 | 0.005 | |
| groupComparisonPTM | 4.074 | 0.090 | 4.158 | |
| groupComparisonPlotsPTM | 13.419 | 0.123 | 13.538 | |
| locateMod | 0.000 | 0.001 | 0.000 | |
| locatePTM | 0.012 | 0.003 | 0.015 | |
| maxq_lf_annotation | 0.002 | 0.000 | 0.002 | |
| maxq_lf_evidence | 0.006 | 0.004 | 0.010 | |
| maxq_tmt_annotation | 0.002 | 0.000 | 0.002 | |
| maxq_tmt_evidence | 0.012 | 0.003 | 0.015 | |
| pd_annotation | 0.001 | 0.000 | 0.001 | |
| pd_psm_input | 0.009 | 0.002 | 0.010 | |
| pd_testing_output | 0.083 | 0.175 | 0.259 | |
| raw.input | 0.048 | 0.000 | 0.048 | |
| raw.input.tmt | 0.004 | 0.001 | 0.005 | |
| spectronaut_annotation | 0.001 | 0.000 | 0.001 | |
| spectronaut_input | 0.002 | 0.001 | 0.004 | |
| summary.data | 0.183 | 0.446 | 0.629 | |
| summary.data.tmt | 0.336 | 0.875 | 1.212 | |
| tidyFasta | 0.007 | 0.000 | 0.008 | |