Anthony Wu
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/MSstatsPTM |
| git_branch: devel |
| git_last_commit: 3cf3b26 |
| git_last_commit_date: 2025-08-04 18:17:37 -0400 (Mon, 04 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1376/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 2.11.4 (landing page) Anthony Wu
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 2.11.4 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MSstatsPTM_2.11.4.tar.gz |
| StartedAt: 2025-08-15 05:37:52 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 05:42:39 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 287.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstatsPTM.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsPTM.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MSstatsPTM_2.11.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/MSstatsPTM.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsPTM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsPTM' version '2.11.4'
* 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 whether package 'MSstatsPTM' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 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'
.plot.profile.summary.tmt: no visible binding for global variable
'CENSORED'
.plot.profile.tmt: no visible binding for global variable 'CENSORED'
.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 CENSORED
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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/MSstatsPTM/libs/x64/MSstatsPTM.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
groupComparisonPlotsPTM 14.19 0.26 14.47
designSampleSizePTM 6.75 0.11 6.86
groupComparisonPTM 5.67 0.16 5.83
dataSummarizationPTM_TMT 4.86 0.19 5.14
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
'F:/biocbuild/bbs-3.22-bioc/meat/MSstatsPTM.Rcheck/00check.log'
for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'MSstatsPTM' ... ** this is package 'MSstatsPTM' version '2.11.4' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++17 -shared -s -static-libgcc -o MSstatsPTM.dll tmp.def RcppExports.o model_adjustment.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs/x64 ** 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 ** 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 version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 [2025-08-15 05:41:43] ** Raw data from MaxQuant imported successfully.
INFO [2025-08-15 05:41:43] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-08-15 05:41:43] ** Rows with values of Reverse equal to + are removed
INFO [2025-08-15 05:41:43] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:43] ** Using provided annotation.
INFO [2025-08-15 05:41:43] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:43] ** 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 [2025-08-15 05:41:43] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:43] ** Shared peptides are removed.
INFO [2025-08-15 05:41:43] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:43] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:43] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:43] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:43] ** Fractionation handled.
INFO [2025-08-15 05:41:43] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:43] ** 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 [2025-08-15 05:41:44] ** Raw data from MaxQuant imported successfully.
INFO [2025-08-15 05:41:44] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-08-15 05:41:44] ** Rows with values of Reverse equal to + are removed
INFO [2025-08-15 05:41:44] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:44] ** Using provided annotation.
INFO [2025-08-15 05:41:44] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:44] ** 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 within each run will be kept.
INFO [2025-08-15 05:41:44] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:44] ** Shared peptides are removed.
INFO [2025-08-15 05:41:44] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:44] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:44] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:44] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:44] ** Fractionation handled.
INFO [2025-08-15 05:41:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:44] ** 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 [2025-08-15 05:41:44] ** Raw data from MaxQuant imported successfully.
INFO [2025-08-15 05:41:44] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-08-15 05:41:44] ** Rows with values of Reverse equal to + are removed
INFO [2025-08-15 05:41:44] ** Using provided annotation.
INFO [2025-08-15 05:41:44] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:44] ** 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 [2025-08-15 05:41:44] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:44] ** Shared peptides are removed.
INFO [2025-08-15 05:41:44] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:44] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:44] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:44] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:44] ** Fractionation handled.
INFO [2025-08-15 05:41:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:44] ** 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 [2025-08-15 05:41:44] ** Raw data from MaxQuant imported successfully.
INFO [2025-08-15 05:41:44] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2025-08-15 05:41:44] ** Rows with values of Reverse equal to + are removed
INFO [2025-08-15 05:41:44] ** Using provided annotation.
INFO [2025-08-15 05:41:44] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:44] ** 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 [2025-08-15 05:41:44] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:44] ** Shared peptides are removed.
INFO [2025-08-15 05:41:44] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:44] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:44] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:44] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:44] ** Fractionation handled.
INFO [2025-08-15 05:41:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:44] ** 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 [2025-08-15 05:41:47] ** Raw data from Spectronaut imported successfully.
INFO [2025-08-15 05:41:47] ** Raw data from Spectronaut cleaned successfully.
INFO [2025-08-15 05:41:47] ** Using provided annotation.
INFO [2025-08-15 05:41:47] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:47] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
WARN [2025-08-15 05:41:47] ** PGQvalue not found in input columns.
WARN [2025-08-15 05:41:47] ** EGQvalue not found in input columns.
INFO [2025-08-15 05:41:47] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:47] ** Shared peptides are removed.
INFO [2025-08-15 05:41:47] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:47] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:47] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:47] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:47] ** Fractionation handled.
INFO [2025-08-15 05:41:47] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:47] ** 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 [2025-08-15 05:41:49] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:49] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:49] ** Using provided annotation.
INFO [2025-08-15 05:41:49] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:49] ** 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 across runs will be removed.
INFO [2025-08-15 05:41:49] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:49] ** Shared peptides are removed.
INFO [2025-08-15 05:41:49] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:49] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:49] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:49] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:49] ** Fractionation handled.
INFO [2025-08-15 05:41:49] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:49] ** 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 [2025-08-15 05:41:50] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:50] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:50] ** Using provided annotation.
INFO [2025-08-15 05:41:50] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:50] ** 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 across runs will be removed.
INFO [2025-08-15 05:41:50] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:50] ** Shared peptides are removed.
INFO [2025-08-15 05:41:50] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:50] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:50] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:51] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:51] ** Fractionation handled.
INFO [2025-08-15 05:41:51] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:51] ** 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 [2025-08-15 05:41:52] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:52] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:52] ** Using provided annotation.
INFO [2025-08-15 05:41:52] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:52] ** 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 [2025-08-15 05:41:52] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:52] ** Shared peptides are removed.
INFO [2025-08-15 05:41:52] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:52] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:52] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:52] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:52] ** Fractionation handled.
INFO [2025-08-15 05:41:52] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:52] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 48 tests [0;32mOK[0m INFO [2025-08-15 05:41:53] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:53] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:53] ** Using provided annotation.
INFO [2025-08-15 05:41:53] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:53] ** 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 [2025-08-15 05:41:53] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:53] ** Shared peptides are removed.
INFO [2025-08-15 05:41:53] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:53] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:53] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:54] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:54] ** Fractionation handled.
INFO [2025-08-15 05:41:54] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:54] ** 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 [2025-08-15 05:41:55] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:55] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:55] ** Using provided annotation.
INFO [2025-08-15 05:41:55] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:55] ** 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 [2025-08-15 05:41:55] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:55] ** Shared peptides are removed.
INFO [2025-08-15 05:41:55] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:55] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:55] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:55] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:55] ** Fractionation handled.
INFO [2025-08-15 05:41:55] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:55] ** 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 [2025-08-15 05:41:55] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:55] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:55] ** Using provided annotation.
INFO [2025-08-15 05:41:55] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:55] ** 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 [2025-08-15 05:41:55] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:55] ** Shared peptides are removed.
INFO [2025-08-15 05:41:55] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:55] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:55] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:55] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:55] ** Fractionation handled.
INFO [2025-08-15 05:41:55] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:55] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-08-15 05:41:55] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2025-08-15 05:41:55] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2025-08-15 05:41:55] ** Using provided annotation.
INFO [2025-08-15 05:41:55] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:55] ** 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 [2025-08-15 05:41:55] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:55] ** Shared peptides are removed.
INFO [2025-08-15 05:41:55] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:55] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:55] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:55] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO [2025-08-15 05:41:55] ** Fractions belonging to same mixture have been combined.
INFO [2025-08-15 05:41:55] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:55] ** Fractionation handled.
INFO [2025-08-15 05:41:55] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:55] ** 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 [2025-08-15 05:41:56] ** Raw data from Metamorpheus imported successfully.
INFO [2025-08-15 05:41:56] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-08-15 05:41:56] ** Using provided annotation.
INFO [2025-08-15 05:41:56] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:56] ** 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 [2025-08-15 05:41:56] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Shared peptides are removed.
INFO [2025-08-15 05:41:56] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:56] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:56] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Fractionation handled.
INFO [2025-08-15 05:41:56] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:56] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO [2025-08-15 05:41:56] ** Raw data from Metamorpheus imported successfully.
INFO [2025-08-15 05:41:56] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-08-15 05:41:56] ** Using provided annotation.
INFO [2025-08-15 05:41:56] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:56] ** 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 [2025-08-15 05:41:56] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Shared peptides are removed.
INFO [2025-08-15 05:41:56] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:56] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:56] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Fractionation handled.
INFO [2025-08-15 05:41:56] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:56] ** 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 [2025-08-15 05:41:56] ** Raw data from Metamorpheus imported successfully.
INFO [2025-08-15 05:41:56] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-08-15 05:41:56] ** Using provided annotation.
INFO [2025-08-15 05:41:56] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:56] ** 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 [2025-08-15 05:41:56] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Shared peptides are removed.
INFO [2025-08-15 05:41:56] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:56] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:56] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:56] ** Fractionation handled.
INFO [2025-08-15 05:41:56] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:56] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO [2025-08-15 05:41:56] ** Raw data from Metamorpheus imported successfully.
INFO [2025-08-15 05:41:57] ** Raw data from Metamorpheus cleaned successfully.
INFO [2025-08-15 05:41:57] ** Using provided annotation.
INFO [2025-08-15 05:41:57] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:57] ** 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 [2025-08-15 05:41:57] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:57] ** Shared peptides are removed.
INFO [2025-08-15 05:41:57] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:57] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:57] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:57] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:57] ** Fractionation handled.
INFO [2025-08-15 05:41:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:57] ** 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 [2025-08-15 05:41:57] ** Raw data from Progenesis imported successfully.
INFO [2025-08-15 05:41:57] ** Raw data from Progenesis cleaned successfully.
INFO [2025-08-15 05:41:57] ** Using provided annotation.
INFO [2025-08-15 05:41:57] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:57] ** 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 [2025-08-15 05:41:57] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:57] ** Shared peptides are removed.
INFO [2025-08-15 05:41:57] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2025-08-15 05:41:57] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:57] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:57] ** Features with one or two measurements across runs are removed.
INFO [2025-08-15 05:41:57] ** Fractionation handled.
INFO [2025-08-15 05:41:57] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:57] ** 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 [2025-08-15 05:41:58] ** Raw data from Philosopher imported successfully.
INFO [2025-08-15 05:41:58] ** Using provided annotation.
INFO [2025-08-15 05:41:58] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:58] ** 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 [2025-08-15 05:41:58] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2025-08-15 05:41:58] ** PeptideProphetProbability not found in input columns.
INFO [2025-08-15 05:41:58] ** Sequences containing Oxidation are removed.
INFO [2025-08-15 05:41:58] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:58] ** Shared peptides are removed.
INFO [2025-08-15 05:41:58] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:58] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:58] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:58] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:58] ** Fractionation handled.
INFO [2025-08-15 05:41:58] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:58] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-08-15 05:41:58] ** Raw data from Philosopher imported successfully.
test_converters.R............. 85 tests [0;32mOK[0m
test_converters.R............. 86 tests [0;32mOK[0m INFO [2025-08-15 05:41:59] ** Raw data from Philosopher imported successfully.
INFO [2025-08-15 05:41:59] ** Using provided annotation.
INFO [2025-08-15 05:41:59] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:59] ** 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 [2025-08-15 05:41:59] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2025-08-15 05:41:59] ** PeptideProphetProbability not found in input columns.
INFO [2025-08-15 05:41:59] ** Sequences containing Oxidation are removed.
INFO [2025-08-15 05:41:59] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:59] ** Shared peptides are removed.
INFO [2025-08-15 05:41:59] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:59] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:59] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:59] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:59] ** Fractionation handled.
INFO [2025-08-15 05:41:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:59] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-08-15 05:41:59] ** Raw data from Philosopher imported successfully.
INFO [2025-08-15 05:41:59] ** Using provided annotation.
INFO [2025-08-15 05:41:59] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:59] ** 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 [2025-08-15 05:41:59] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2025-08-15 05:41:59] ** PeptideProphetProbability not found in input columns.
INFO [2025-08-15 05:41:59] ** Sequences containing Oxidation are removed.
INFO [2025-08-15 05:41:59] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:59] ** Shared peptides are removed.
INFO [2025-08-15 05:41:59] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:41:59] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:41:59] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:59] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:41:59] ** Fractionation handled.
INFO [2025-08-15 05:41:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:59] ** 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 [2025-08-15 05:41:59] ** Raw data from FragPipe imported successfully.
INFO [2025-08-15 05:41:59] ** Using annotation extracted from quantification data.
INFO [2025-08-15 05:41:59] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:41:59] ** 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 [2025-08-15 05:41:59] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:59] ** Shared peptides are removed.
INFO [2025-08-15 05:41:59] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2025-08-15 05:41:59] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:59] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:41:59] ** Features with all missing measurements across runs are removed.
INFO [2025-08-15 05:41:59] ** Fractionation handled.
INFO [2025-08-15 05:41:59] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:41:59] ** 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 [2025-08-15 05:42:01] ** Raw data from ProteinProspector imported successfully.
INFO [2025-08-15 05:42:01] ** Raw data from ProteinProspector cleaned successfully.
INFO [2025-08-15 05:42:01] ** Using provided annotation.
INFO [2025-08-15 05:42:01] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:42:01] ** 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 [2025-08-15 05:42:01] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:42:01] ** Shared peptides are removed.
INFO [2025-08-15 05:42:01] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:42:01] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:42:01] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:42:01] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO [2025-08-15 05:42:01] ** Fractions belonging to same mixture have been combined.
INFO [2025-08-15 05:42:01] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:42:01] ** Fractionation handled.
INFO [2025-08-15 05:42:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:42:01] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2025-08-15 05:42:01] ** Raw data from ProteinProspector imported successfully.
INFO [2025-08-15 05:42:01] ** Raw data from ProteinProspector cleaned successfully.
INFO [2025-08-15 05:42:01] ** Using provided annotation.
INFO [2025-08-15 05:42:01] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2025-08-15 05:42:01] ** 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 [2025-08-15 05:42:01] ** Features with all missing measurements across channels within each run are removed.
INFO [2025-08-15 05:42:01] ** Shared peptides are removed.
INFO [2025-08-15 05:42:01] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:42:01] ** PSMs have been aggregated to peptide ions.
INFO [2025-08-15 05:42:01] ** Run annotation merged with quantification data.
INFO [2025-08-15 05:42:01] ** For peptides overlapped between fractions of Mixture1_1 use the fraction with maximal average abundance.
INFO [2025-08-15 05:42:01] ** Fractions belonging to same mixture have been combined.
INFO [2025-08-15 05:42:01] ** Features with one or two measurements across channels within each run are removed.
INFO [2025-08-15 05:42:01] ** Fractionation handled.
INFO [2025-08-15 05:42:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2025-08-15 05:42:01] ** 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;34m19.2s[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;34m0.3s[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;34m0.3s[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 [2025-08-15 05:42:08] == Start to test and get inference in whole plot ...
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INFO [2025-08-15 05:42:13] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2025-08-15 05:42:13] == Start to test and get inference in whole plot ...
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INFO [2025-08-15 05:42:14] == 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 [2025-08-15 05:42:14] Design: 2 mixtures.
INFO [2025-08-15 05:42:14] Design: 1 MS run per mixture.
INFO [2025-08-15 05:42:14] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2025-08-15 05:42:14] Model fitting for 90 proteins.
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INFO [2025-08-15 05:42:18] Testing for 90 proteins:
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Starting Protein modeling...
INFO [2025-08-15 05:42:18] Design: 2 mixtures.
INFO [2025-08-15 05:42:18] Design: 1 MS run per mixture.
INFO [2025-08-15 05:42:18] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2025-08-15 05:42:18] Model fitting for 85 proteins.
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INFO [2025-08-15 05:42:25] 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;34m24.3s[0m
All ok, 190 results (44.2s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
49.26 2.37 52.06
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsPTMFormat | 0.31 | 0.02 | 0.32 | |
| FragPipetoMSstatsPTMFormat | 1.35 | 0.04 | 1.40 | |
| MSstatsPTMSiteLocator | 0 | 0 | 0 | |
| MaxQtoMSstatsPTMFormat | 0.48 | 0.06 | 0.56 | |
| MetamorpheusToMSstatsPTMFormat | 0.16 | 0.05 | 0.21 | |
| PDtoMSstatsPTMFormat | 1.58 | 0.19 | 1.79 | |
| PStoMSstatsPTMFormat | 0.06 | 0.00 | 0.07 | |
| ProgenesistoMSstatsPTMFormat | 0.06 | 0.00 | 0.06 | |
| ProteinProspectortoMSstatsPTMFormat | 0.61 | 0.02 | 0.63 | |
| SkylinetoMSstatsPTMFormat | 0.05 | 0.01 | 0.06 | |
| SpectronauttoMSstatsPTMFormat | 0.69 | 0.03 | 0.75 | |
| annotSite | 0 | 0 | 0 | |
| dataProcessPlotsPTM | 2.71 | 0.05 | 2.78 | |
| dataSummarizationPTM | 3.05 | 0.04 | 3.11 | |
| dataSummarizationPTM_TMT | 4.86 | 0.19 | 5.14 | |
| designSampleSizePTM | 6.75 | 0.11 | 6.86 | |
| fragpipe_annotation | 0 | 0 | 0 | |
| fragpipe_annotation_protein | 0.02 | 0.00 | 0.01 | |
| fragpipe_input | 0 | 0 | 0 | |
| fragpipe_input_protein | 0 | 0 | 0 | |
| groupComparisonPTM | 5.67 | 0.16 | 5.83 | |
| groupComparisonPlotsPTM | 14.19 | 0.26 | 14.47 | |
| locateMod | 0 | 0 | 0 | |
| locatePTM | 0.02 | 0.00 | 0.01 | |
| maxq_lf_annotation | 0 | 0 | 0 | |
| maxq_lf_evidence | 0.01 | 0.00 | 0.02 | |
| maxq_tmt_annotation | 0 | 0 | 0 | |
| maxq_tmt_evidence | 0.02 | 0.00 | 0.01 | |
| pd_annotation | 0 | 0 | 0 | |
| pd_psm_input | 0.01 | 0.00 | 0.02 | |
| pd_testing_output | 0.30 | 0.08 | 0.37 | |
| raw.input | 0.08 | 0.00 | 0.08 | |
| raw.input.tmt | 0 | 0 | 0 | |
| spectronaut_annotation | 0 | 0 | 0 | |
| spectronaut_input | 0 | 0 | 0 | |
| summary.data | 0.68 | 0.19 | 0.86 | |
| summary.data.tmt | 1.03 | 0.31 | 1.34 | |
| tidyFasta | 0 | 0 | 0 | |