Devon Kohler
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MSstatsPTM |
| git_branch: RELEASE_3_20 |
| git_last_commit: 04cd9d1 |
| git_last_commit_date: 2024-11-25 15:52:20 -0500 (Mon, 25 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 1355/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 2.8.1 (landing page) Devon Kohler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 2.8.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.8.1.tar.gz |
| StartedAt: 2024-12-21 02:35:58 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 02:39:39 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 220.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsPTM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsPTM_2.8.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.8.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsPTM’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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’
.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’
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’
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 text.angle
which.proteinid.ptm
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-fixTerminus.Rd':
‘fasta_file’
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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
groupComparisonPlotsPTM 10.762 0.108 10.691
dataSummarizationPTM_TMT 6.388 0.412 4.573
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MSstatsPTM’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c model_adjustment.cpp -o model_adjustment.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsPTM)
MSstatsPTM.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(mockery)
> library(MSstatsPTM)
>
> test_check("MSstatsPTM")
Drew the Quality Contol plot(boxplot) for all ptms/proteins.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
>
> proc.time()
user system elapsed
6.876 0.365 7.028
MSstatsPTM.Rcheck/tests/tinytest.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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 [2024-12-21 02:39:01] ** Raw data from MaxQuant imported successfully.
INFO [2024-12-21 02:39:01] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-21 02:39:01] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-21 02:39:01] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:01] ** Using provided annotation.
INFO [2024-12-21 02:39:01] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:01] ** 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 kept.
INFO [2024-12-21 02:39:01] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:01] ** Shared peptides are removed.
INFO [2024-12-21 02:39:01] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:01] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-21 02:39:01] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:01] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:01] ** Fractionation handled.
INFO [2024-12-21 02:39:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:01] ** 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
test_converters.R............. 12 tests [0;32mOK[0m
test_converters.R............. 12 tests [0;32mOK[0m
test_converters.R............. 13 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 INFO [2024-12-21 02:39:01] ** Raw data from MaxQuant imported successfully.
INFO [2024-12-21 02:39:01] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-21 02:39:01] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-21 02:39:01] ** Using provided annotation.
INFO [2024-12-21 02:39:01] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:01] ** 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 across runs will be removed.
INFO [2024-12-21 02:39:01] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:01] ** Shared peptides are removed.
INFO [2024-12-21 02:39:01] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:01] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:01] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:01] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:01] ** Fractionation handled.
INFO [2024-12-21 02:39:01] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:01] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 17 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
test_converters.R............. 23 tests [0;32mOK[0m
test_converters.R............. 24 tests [0;32mOK[0m
test_converters.R............. 24 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 INFO [2024-12-21 02:39:04] ** Raw data from Spectronaut imported successfully.
INFO [2024-12-21 02:39:04] ** Raw data from Spectronaut cleaned successfully.
INFO [2024-12-21 02:39:04] ** Using provided annotation.
INFO [2024-12-21 02:39:04] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:04] ** 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 [2024-12-21 02:39:04] ** PGQvalue not found in input columns.
WARN [2024-12-21 02:39:04] ** EGQvalue not found in input columns.
INFO [2024-12-21 02:39:04] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:04] ** Shared peptides are removed.
INFO [2024-12-21 02:39:04] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:04] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:04] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:04] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:04] ** Fractionation handled.
INFO [2024-12-21 02:39:04] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:04] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 28 tests [0;32mOK[0m
test_converters.R............. 30 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............. 35 tests [0;32mOK[0m
test_converters.R............. 35 tests [0;32mOK[0m
test_converters.R............. 35 tests [0;32mOK[0m
test_converters.R............. 35 tests [0;32mOK[0m INFO [2024-12-21 02:39:05] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:05] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:05] ** Using provided annotation.
INFO [2024-12-21 02:39:05] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:05] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:05] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:05] ** Shared peptides are removed.
INFO [2024-12-21 02:39:05] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:05] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:05] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:05] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:05] ** Fractionation handled.
INFO [2024-12-21 02:39:05] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:05] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 36 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2024-12-21 02:39:06] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:06] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:06] ** Using provided annotation.
INFO [2024-12-21 02:39:06] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:06] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:06] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:06] ** Shared peptides are removed.
INFO [2024-12-21 02:39:06] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:06] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:06] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:06] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:06] ** Fractionation handled.
INFO [2024-12-21 02:39:06] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:06] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 37 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2024-12-21 02:39:06] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:06] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:06] ** Using provided annotation.
INFO [2024-12-21 02:39:06] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:06] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:06] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:07] ** Shared peptides are removed.
INFO [2024-12-21 02:39:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:07] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:07] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:07] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:07] ** Fractionation handled.
INFO [2024-12-21 02:39:07] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:07] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 38 tests [0;32mOK[0m INFO [2024-12-21 02:39:07] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:07] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:07] ** Using provided annotation.
INFO [2024-12-21 02:39:07] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:07] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:07] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:07] ** Shared peptides are removed.
INFO [2024-12-21 02:39:07] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:07] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:07] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:07] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:07] ** Fractionation handled.
INFO [2024-12-21 02:39:07] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:07] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 39 tests [0;32mOK[0m
test_converters.R............. 40 tests [0;32mOK[0m INFO [2024-12-21 02:39:08] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:08] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:08] ** Using provided annotation.
INFO [2024-12-21 02:39:08] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:08] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:08] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:08] ** Shared peptides are removed.
INFO [2024-12-21 02:39:08] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:08] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:08] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:08] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:08] ** Fractionation handled.
INFO [2024-12-21 02:39:08] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:08] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
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............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 43 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2024-12-21 02:39:08] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:08] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:08] ** Using provided annotation.
INFO [2024-12-21 02:39:08] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:08] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2024-12-21 02:39:08] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:08] ** Shared peptides are removed.
INFO [2024-12-21 02:39:08] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:08] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-21 02:39:08] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:08] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:08] ** Fractionation handled.
INFO [2024-12-21 02:39:08] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:08] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2024-12-21 02:39:08] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-21 02:39:08] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-21 02:39:08] ** Using provided annotation.
INFO [2024-12-21 02:39:08] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:08] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2024-12-21 02:39:08] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:08] ** Shared peptides are removed.
INFO [2024-12-21 02:39:08] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:08] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-21 02:39:08] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:08] ** For peptides overlapped between fractions of mixture1_1 use the fraction with maximal average abundance.
INFO [2024-12-21 02:39:08] ** Fractions belonging to same mixture have been combined.
INFO [2024-12-21 02:39:08] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:08] ** Fractionation handled.
INFO [2024-12-21 02:39:08] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:08] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 43 tests [0;32mOK[0m
test_converters.R............. 45 tests [0;32mOK[0m
test_converters.R............. 46 tests [0;32mOK[0m
test_converters.R............. 47 tests [0;32mOK[0m
test_converters.R............. 48 tests [0;32mOK[0m
test_converters.R............. 49 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
test_converters.R............. 50 tests [0;32mOK[0m
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............. 54 tests [0;32mOK[0m
test_converters.R............. 55 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus imported successfully.
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus cleaned successfully.
INFO [2024-12-21 02:39:09] ** Using provided annotation.
INFO [2024-12-21 02:39:09] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:09] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:09] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Shared peptides are removed.
INFO [2024-12-21 02:39:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Fractionation handled.
INFO [2024-12-21 02:39:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:09] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus imported successfully.
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus cleaned successfully.
INFO [2024-12-21 02:39:09] ** Using provided annotation.
INFO [2024-12-21 02:39:09] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:09] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:09] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Shared peptides are removed.
INFO [2024-12-21 02:39:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Fractionation handled.
INFO [2024-12-21 02:39:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:09] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 55 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............. 61 tests [0;32mOK[0m
test_converters.R............. 62 tests [0;32mOK[0m [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus imported successfully.
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus cleaned successfully.
INFO [2024-12-21 02:39:09] ** Using provided annotation.
INFO [2024-12-21 02:39:09] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:09] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:09] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Shared peptides are removed.
INFO [2024-12-21 02:39:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Fractionation handled.
INFO [2024-12-21 02:39:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:09] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus imported successfully.
INFO [2024-12-21 02:39:09] ** Raw data from Metamorpheus cleaned successfully.
INFO [2024-12-21 02:39:09] ** Using provided annotation.
INFO [2024-12-21 02:39:09] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:09] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:09] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Shared peptides are removed.
INFO [2024-12-21 02:39:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Fractionation handled.
INFO [2024-12-21 02:39:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:09] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 62 tests [0;32mOK[0m
test_converters.R............. 64 tests [0;32mOK[0m
test_converters.R............. 65 tests [0;32mOK[0m
test_converters.R............. 66 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............. 69 tests [0;32mOK[0m
test_converters.R............. 69 tests [0;32mOK[0m
test_converters.R............. 69 tests [0;32mOK[0m
test_converters.R............. 69 tests [0;32mOK[0m
test_converters.R............. 69 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 INFO [2024-12-21 02:39:09] ** Raw data from Progenesis imported successfully.
INFO [2024-12-21 02:39:09] ** Raw data from Progenesis cleaned successfully.
INFO [2024-12-21 02:39:09] ** Using provided annotation.
INFO [2024-12-21 02:39:09] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:09] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-12-21 02:39:09] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Shared peptides are removed.
INFO [2024-12-21 02:39:09] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:09] ** Features with one or two measurements across runs are removed.
INFO [2024-12-21 02:39:09] ** Fractionation handled.
INFO [2024-12-21 02:39:09] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:09] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 71 tests [0;32mOK[0m
test_converters.R............. 72 tests [0;32mOK[0m
test_converters.R............. 73 tests [0;32mOK[0m
test_converters.R............. 74 tests [0;32mOK[0m INFO [2024-12-21 02:39:10] ** Raw data from Philosopher imported successfully.
INFO [2024-12-21 02:39:10] ** Using provided annotation.
INFO [2024-12-21 02:39:10] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:10] ** 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 [2024-12-21 02:39:10] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2024-12-21 02:39:10] ** PeptideProphetProbability not found in input columns.
INFO [2024-12-21 02:39:10] ** Sequences containing Oxidation are removed.
INFO [2024-12-21 02:39:10] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:10] ** Shared peptides are removed.
INFO [2024-12-21 02:39:10] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:10] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-21 02:39:10] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:10] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:10] ** Fractionation handled.
INFO [2024-12-21 02:39:10] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:10] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2024-12-21 02:39:10] ** Raw data from Philosopher imported successfully.
test_converters.R............. 75 tests [0;32mOK[0m
test_converters.R............. 76 tests [0;32mOK[0m INFO [2024-12-21 02:39:10] ** Raw data from Philosopher imported successfully.
INFO [2024-12-21 02:39:10] ** Using provided annotation.
INFO [2024-12-21 02:39:10] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:10] ** 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 [2024-12-21 02:39:10] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2024-12-21 02:39:10] ** PeptideProphetProbability not found in input columns.
INFO [2024-12-21 02:39:10] ** Sequences containing Oxidation are removed.
INFO [2024-12-21 02:39:10] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:10] ** Shared peptides are removed.
INFO [2024-12-21 02:39:10] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:10] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-21 02:39:11] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:11] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:11] ** Fractionation handled.
INFO [2024-12-21 02:39:11] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:11] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
INFO [2024-12-21 02:39:11] ** Raw data from Philosopher imported successfully.
INFO [2024-12-21 02:39:11] ** Using provided annotation.
INFO [2024-12-21 02:39:11] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:11] ** 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 [2024-12-21 02:39:11] ** Rows with values not greater than 0.6 in Purity are removed
WARN [2024-12-21 02:39:11] ** PeptideProphetProbability not found in input columns.
INFO [2024-12-21 02:39:11] ** Sequences containing Oxidation are removed.
INFO [2024-12-21 02:39:11] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:11] ** Shared peptides are removed.
INFO [2024-12-21 02:39:11] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-21 02:39:11] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-21 02:39:11] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:11] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-21 02:39:11] ** Fractionation handled.
INFO [2024-12-21 02:39:11] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:11] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
test_converters.R............. 76 tests [0;32mOK[0m
test_converters.R............. 78 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
test_converters.R............. 82 tests [0;32mOK[0m
test_converters.R............. 83 tests [0;32mOK[0m
test_converters.R............. 83 tests [0;32mOK[0m
test_converters.R............. 83 tests [0;32mOK[0m
test_converters.R............. 83 tests [0;32mOK[0m
test_converters.R............. 83 tests [0;32mOK[0m
test_converters.R............. 84 tests [0;32mOK[0m
test_converters.R............. 85 tests [0;32mOK[0m INFO [2024-12-21 02:39:11] ** Raw data from FragPipe imported successfully.
INFO [2024-12-21 02:39:11] ** Using annotation extracted from quantification data.
INFO [2024-12-21 02:39:11] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-21 02:39:11] ** 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 [2024-12-21 02:39:11] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:11] ** Shared peptides are removed.
INFO [2024-12-21 02:39:11] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2024-12-21 02:39:11] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:11] ** Run annotation merged with quantification data.
INFO [2024-12-21 02:39:11] ** Features with all missing measurements across runs are removed.
INFO [2024-12-21 02:39:11] ** Fractionation handled.
INFO [2024-12-21 02:39:11] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-21 02:39:11] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 85 tests [0;32mOK[0m
test_converters.R............. 86 tests [0;32mOK[0m
test_converters.R............. 87 tests [0;32mOK[0m
test_converters.R............. 88 tests [0;32mOK[0m [0;34m11.2s[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;34m0.2s[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 [2024-12-21 02:39:15] == Start to test and get inference in whole plot ...
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INFO [2024-12-21 02:39:19] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2024-12-21 02:39:19] == Start to test and get inference in whole plot ...
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INFO [2024-12-21 02:39:20] == Comparisons for all proteins are done.
Starting adjustment...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 4 tests [0;32mOK[0m
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test_groupComparisonPTM.R..... 9 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m Starting PTM modeling...
INFO [2024-12-21 02:39:20] Design: 2 mixtures.
INFO [2024-12-21 02:39:20] Design: 1 MS run per mixture.
INFO [2024-12-21 02:39:20] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2024-12-21 02:39:20] Model fitting for 90 proteins.
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INFO [2024-12-21 02:39:22] Testing for 90 proteins:
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Starting Protein modeling...
INFO [2024-12-21 02:39:23] Design: 2 mixtures.
INFO [2024-12-21 02:39:23] Design: 1 MS run per mixture.
INFO [2024-12-21 02:39:23] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2024-12-21 02:39:23] Model fitting for 85 proteins.
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INFO [2024-12-21 02:39:28] 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;34m16.7s[0m
All ok, 167 results (28.4s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
40.581 2.099 34.423
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsPTMFormat | 0 | 0 | 0 | |
| FragPipetoMSstatsPTMFormat | 0.492 | 0.054 | 0.340 | |
| MSstatsPTMSiteLocator | 0 | 0 | 0 | |
| MaxQtoMSstatsPTMFormat | 1.219 | 0.091 | 0.895 | |
| MetamorpheusToMSstatsPTMFormat | 0.282 | 0.036 | 0.165 | |
| PDtoMSstatsPTMFormat | 1.394 | 0.137 | 0.969 | |
| PStoMSstatsPTMFormat | 0.145 | 0.012 | 0.081 | |
| ProgenesistoMSstatsPTMFormat | 0.117 | 0.015 | 0.069 | |
| SkylinetoMSstatsPTMFormat | 0.092 | 0.006 | 0.050 | |
| SpectronauttoMSstatsPTMFormat | 1.113 | 0.080 | 0.712 | |
| annotSite | 0.001 | 0.001 | 0.001 | |
| dataProcessPlotsPTM | 2.466 | 0.072 | 2.141 | |
| dataSummarizationPTM | 2.828 | 0.147 | 2.339 | |
| dataSummarizationPTM_TMT | 6.388 | 0.412 | 4.573 | |
| designSampleSizePTM | 4.342 | 0.087 | 4.218 | |
| fragpipe_annotation | 0.002 | 0.000 | 0.002 | |
| fragpipe_annotation_protein | 0.002 | 0.001 | 0.002 | |
| fragpipe_input | 0.004 | 0.002 | 0.006 | |
| fragpipe_input_protein | 0.004 | 0.002 | 0.006 | |
| groupComparisonPTM | 4.672 | 0.074 | 4.572 | |
| groupComparisonPlotsPTM | 10.762 | 0.108 | 10.691 | |
| locateMod | 0.001 | 0.000 | 0.000 | |
| locatePTM | 0.020 | 0.001 | 0.022 | |
| maxq_lf_annotation | 0.002 | 0.000 | 0.003 | |
| maxq_lf_evidence | 0.010 | 0.002 | 0.013 | |
| maxq_tmt_annotation | 0.002 | 0.000 | 0.002 | |
| maxq_tmt_evidence | 0.014 | 0.004 | 0.017 | |
| pd_annotation | 0.001 | 0.001 | 0.002 | |
| pd_psm_input | 0.011 | 0.002 | 0.013 | |
| pd_testing_output | 0.170 | 0.142 | 0.312 | |
| raw.input | 0.040 | 0.001 | 0.041 | |
| raw.input.tmt | 0.004 | 0.000 | 0.005 | |
| spectronaut_annotation | 0.002 | 0.000 | 0.002 | |
| spectronaut_input | 0.004 | 0.001 | 0.005 | |
| summary.data | 0.328 | 0.363 | 0.694 | |
| summary.data.tmt | 0.659 | 0.709 | 1.381 | |
| tidyFasta | 0.008 | 0.001 | 0.009 | |