Devon Kohler
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MSstatsShiny |
| git_branch: RELEASE_3_17 |
| git_last_commit: 6150f39 |
| git_last_commit_date: 2023-09-08 11:01:03 -0400 (Fri, 08 Sep 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:33 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1322/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsShiny 1.2.5 (landing page) Devon Kohler
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the MSstatsShiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsShiny.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MSstatsShiny |
| Version: 1.2.5 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MSstatsShiny_1.2.5.tar.gz |
| StartedAt: 2023-10-15 23:08:22 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 23:11:51 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 209.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsShiny.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MSstatsShiny.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MSstatsShiny_1.2.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MSstatsShiny.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsShiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsShiny’ version ‘1.2.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsShiny’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MSstatsTMT:::.logSum’ ‘MSstatsTMT:::.summarizeSimpleStat’
‘MSstatsTMT:::.summarizeTMP’
‘MSstatsTMT:::MSstatsFitComparisonModelsTMT’
‘MSstatsTMT:::MSstatsGroupComparisonOutputTMT’
‘MSstatsTMT:::MSstatsModerateTTest’
‘MSstatsTMT:::MSstatsNormalizeTMT’
‘MSstatsTMT:::MSstatsPrepareForGroupComparisonTMT’
‘MSstatsTMT:::MSstatsPrepareForSummarizationTMT’
‘MSstatsTMT:::MSstatsSummarizationOutputTMT’
‘MSstatsTMT:::MSstatsTestSingleProteinTMT’
‘MSstatsTMT:::getProcessedTMT’ ‘MSstatsTMT:::getSummarizedTMT’
‘shinyBS:::buildTooltipOrPopoverOptionsList’ ‘shinyBS:::shinyBSDep’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getAnnot: no visible binding for global variable ‘annotation.pd’
getSummary1: no visible binding for global variable ‘Condition’
getSummary1: no visible binding for global variable ‘BioReplicate’
getSummary1: no visible binding for global variable ‘Mixture’
getSummary1: no visible binding for global variable ‘Run’
getSummary1: no visible binding for global variable ‘TechRepMixture’
getSummary1: no visible binding for global variable ‘Fraction’
getSummary1: no visible binding for global variable ‘Condition_Run’
getSummary1: no visible binding for global variable ‘BioReplicate_Run’
getSummary1: no visible binding for global variable ‘Number of
Fractions’
getSummary2: no visible binding for global variable ‘ProteinName’
getSummary2: no visible binding for global variable ‘PeptideSequence’
getSummary2: no visible binding for global variable ‘Charge’
getSummary2: no visible binding for global variable ‘PrecursorCharge’
getSummary2: no visible binding for global variable ‘FragmentIon’
getSummary2: no visible binding for global variable ‘ProductCharge’
getSummary2: no visible binding for global variable ‘FEATURES’
getSummary2: no visible binding for global variable ‘Intensity’
getSummary2: no visible binding for global variable ‘Min_Intensity’
getSummary2: no visible binding for global variable ‘Max_Intensity’
getSummary2: no visible binding for global variable ‘npep’
getSummary2: no visible binding for global variable ‘nfea’
getSummary2: no visible binding for global variable
‘Features_Peptides_min’
getSummary2: no visible binding for global variable
‘Features_Peptides_max’
getSummary2: no visible binding for global variable
‘Peptides_Proteins_min’
getSummary2: no visible binding for global variable
‘Peptides_Proteins_max’
loadpageServer: no visible global function definition for
‘moduleServer’
server: no visible global function definition for ‘callModule’
Undefined global functions or variables:
BioReplicate BioReplicate_Run Charge Condition Condition_Run FEATURES
Features_Peptides_max Features_Peptides_min Fraction FragmentIon
Intensity Max_Intensity Min_Intensity Mixture Number of Fractions
PeptideSequence Peptides_Proteins_max Peptides_Proteins_min
PrecursorCharge ProductCharge ProteinName Run TechRepMixture
annotation.pd callModule moduleServer nfea npep
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tmt_model 6.901 0.192 6.176
tmt_summarization_loop 5.018 0.044 4.144
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘MSstatsShiny_Launch_Instructions.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MSstatsShiny.Rcheck/00check.log’
for details.
MSstatsShiny.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MSstatsShiny ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘MSstatsShiny’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsShiny)
MSstatsShiny.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(mockery)
> library(MSstatsShiny)
>
> test_check("MSstatsShiny")
Loading required package: shiny
Reached in evidence
Reached in evidence
Reached in evidence
Reached in evidence
Reached in unmod
Reached in unmod
Reached in proteins_group
Reached in proteins_group
Reached in proteins_group
Reached in proteins_group
Reached in maxq_ptm_sites
Reached in maxq_ptm_sites
Reached in ump annot
Reached in ump annot
Reached in ump annot
Reached in ump annot
[1] "Inside Annot"
[1] "before reading annot file"
[1] "after reading annot file"
[1] "Inside Annot"
[1] "Inside Annot"
[1] "before reading annot file"
[1] "after reading annot file"
Reached in maxq annot
Reached in maxq annot
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "list"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "list"
[1] "+++++++++ In getData +++++++++"
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is maxq
Reached in maxq
INFO [2023-10-15 23:11:18] ** Raw data from MaxQuant imported successfully.
INFO [2023-10-15 23:11:18] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2023-10-15 23:11:18] ** Rows with values of Reverse equal to + are removed
INFO [2023-10-15 23:11:18] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2023-10-15 23:11:18] ** Rows with values of Reverse equal to + are removed
INFO [2023-10-15 23:11:18] ** Rows with values of Onlyidentifiedbysite equal to + are removed
INFO [2023-10-15 23:11:18] ** + Contaminant, + Reverse, + Potential.contaminant, + Only.identified.by.site proteins are removed.
INFO [2023-10-15 23:11:18] ** Raw data from MaxQuant cleaned successfully.
INFO [2023-10-15 23:11:18] ** Using provided annotation.
INFO [2023-10-15 23:11:18] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:18] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:18] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Shared peptides are removed.
INFO [2023-10-15 23:11:18] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:18] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:18] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Fractionation handled.
INFO [2023-10-15 23:11:18] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:18] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is PD
INFO [2023-10-15 23:11:18] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2023-10-15 23:11:18] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2023-10-15 23:11:18] ** Using provided annotation.
INFO [2023-10-15 23:11:18] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:18] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:18] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Shared peptides are removed.
INFO [2023-10-15 23:11:18] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:18] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:18] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Fractionation handled.
INFO [2023-10-15 23:11:18] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:18] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is prog
Reached in prog
INFO [2023-10-15 23:11:18] ** Raw data from Progenesis imported successfully.
INFO [2023-10-15 23:11:18] ** Raw data from Progenesis cleaned successfully.
INFO [2023-10-15 23:11:18] ** Using provided annotation.
INFO [2023-10-15 23:11:18] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:18] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:18] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Shared peptides are removed.
INFO [2023-10-15 23:11:18] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:18] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:18] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:18] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:18] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:18] ** Fractionation handled.
INFO [2023-10-15 23:11:18] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:18] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sky
Reached here in skyline
INFO [2023-10-15 23:11:19] ** Raw data from Skyline imported successfully.
INFO [2023-10-15 23:11:19] ** Raw data from Skyline cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using annotation extracted from quantification data.
INFO [2023-10-15 23:11:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:19] ** Rows with values of StandardType equal to iRT are removed
INFO [2023-10-15 23:11:19] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2023-10-15 23:11:19] ** DetectionQValue not found in input columns.
INFO [2023-10-15 23:11:19] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-10-15 23:11:19] ** Three isotopic preaks per feature and run are summed
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sky
Reached here in skyline
INFO [2023-10-15 23:11:19] ** Raw data from Skyline imported successfully.
INFO [2023-10-15 23:11:19] ** Raw data from Skyline cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using annotation extracted from quantification data.
INFO [2023-10-15 23:11:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: IsotopeLabelType, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:19] ** Rows with values of StandardType equal to iRT are removed
INFO [2023-10-15 23:11:19] ** Intensities with values of Truncated equal to TRUE are replaced with NA
WARN [2023-10-15 23:11:19] ** DetectionQValue not found in input columns.
INFO [2023-10-15 23:11:19] ** Sequences containing DECOY, Decoys are removed.
INFO [2023-10-15 23:11:19] ** Three isotopic preaks per feature and run are summed
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: sum
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is openms
INFO [2023-10-15 23:11:19] ** Raw data from OpenMS imported successfully.
INFO [2023-10-15 23:11:19] ** Raw data from OpenMS cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using annotation extracted from quantification data.
INFO [2023-10-15 23:11:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is ump
INFO [2023-10-15 23:11:19] ** Raw data from DIAUmpire imported successfully.
INFO [2023-10-15 23:11:19] ** Using selected fragments.
INFO [2023-10-15 23:11:19] ** Extracted the data from selected fragments and/or peptides.
INFO [2023-10-15 23:11:19] ** Raw data from DIAUmpire cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using provided annotation.
INFO [2023-10-15 23:11:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, FragmentIon
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is spec
INFO [2023-10-15 23:11:19] ** Raw data from Spectronaut imported successfully.
INFO [2023-10-15 23:11:19] ** Raw data from Spectronaut cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using annotation extracted from quantification data.
INFO [2023-10-15 23:11:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:19] ** Intensities with values not smaller than 0.01 in PGQvalue are replaced with NA
INFO [2023-10-15 23:11:19] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is open
INFO [2023-10-15 23:11:19] ** Raw data from OpenSWATH imported successfully.
INFO [2023-10-15 23:11:19] ** Raw data from OpenSWATH cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using provided annotation.
INFO [2023-10-15 23:11:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge, FragmentIon
- Shared peptides will be removed.
- Proteins with a single feature will be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2023-10-15 23:11:19] ** Rows with values of decoy equal to 1 are removed
INFO [2023-10-15 23:11:19] ** Rows with values not smaller than 0.01 in m_score are removed
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] Proteins with a single feature are removed.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
Reached in openSwath
[1] "+++++++++ In getData +++++++++"
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is maxq
Reached in maxq
INFO [2023-10-15 23:11:19] ** Raw data from MaxQuant imported successfully.
INFO [2023-10-15 23:11:19] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2023-10-15 23:11:19] ** Rows with values of Reverse equal to + are removed
INFO [2023-10-15 23:11:19] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2023-10-15 23:11:19] ** Rows with values of Reverse equal to + are removed
INFO [2023-10-15 23:11:19] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-10-15 23:11:19] ** Raw data from MaxQuant cleaned successfully.
INFO [2023-10-15 23:11:19] ** Using provided annotation.
INFO [2023-10-15 23:11:19] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-10-15 23:11:19] ** PSMs have been aggregated to peptide ions.
INFO [2023-10-15 23:11:19] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-10-15 23:11:19] ** Fractionation handled.
INFO [2023-10-15 23:11:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:19] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
[1] "ProteinName" "PeptideSequence" "Charge" "PSM"
[5] "Mixture" "TechRepMixture" "Run" "Channel"
[9] "BioReplicate" "Condition" "Intensity"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is openms
INFO [2023-10-15 23:11:19] ** Raw data from OpenMS imported successfully.
INFO [2023-10-15 23:11:19] ** Raw data from OpenMS cleaned successfully.
INFO [2023-10-15 23:11:19] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2023-10-15 23:11:19] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-10-15 23:11:19] ** Shared peptides are removed.
INFO [2023-10-15 23:11:19] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-10-15 23:11:19] ** PSMs have been aggregated to peptide ions.
INFO [2023-10-15 23:11:19] ** For peptides overlapped between fractions of 2_2_2 use the fraction with maximal average abundance.
INFO [2023-10-15 23:11:20] ** For peptides overlapped between fractions of 3_3_3 use the fraction with maximal average abundance.
INFO [2023-10-15 23:11:20] ** Fractions belonging to same mixture have been combined.
INFO [2023-10-15 23:11:20] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-10-15 23:11:20] ** Fractionation handled.
INFO [2023-10-15 23:11:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:20] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
[1] "ProteinName" "PeptideSequence" "Charge" "PSM"
[5] "Mixture" "TechRepMixture" "Run" "Channel"
[9] "BioReplicate" "Condition" "Intensity"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is spmin
INFO [2023-10-15 23:11:20] ** Raw data from SpectroMine imported successfully.
INFO [2023-10-15 23:11:20] ** Raw data from SpectroMine cleaned successfully.
INFO [2023-10-15 23:11:20] ** Using provided annotation.
INFO [2023-10-15 23:11:20] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-10-15 23:11:20] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2023-10-15 23:11:20] ** Intensities with values not smaller than 0.01 in PGQValue are replaced with NA
INFO [2023-10-15 23:11:20] ** Intensities with values not smaller than 0.01 in Qvalue are replaced with NA
INFO [2023-10-15 23:11:20] ** Features with all missing measurements across channels within each run are removed.
INFO [2023-10-15 23:11:20] ** Shared peptides are removed.
INFO [2023-10-15 23:11:20] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-10-15 23:11:20] ** PSMs have been aggregated to peptide ions.
INFO [2023-10-15 23:11:20] ** Run annotation merged with quantification data.
INFO [2023-10-15 23:11:20] ** For peptides overlapped between fractions of 1_1 use the fraction with maximal average abundance.
INFO [2023-10-15 23:11:20] ** Fractions belonging to same mixture have been combined.
INFO [2023-10-15 23:11:20] ** Features with one or two measurements across channels within each run are removed.
INFO [2023-10-15 23:11:20] ** Fractionation handled.
INFO [2023-10-15 23:11:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:20] ** Finished preprocessing. The dataset is ready to be processed by the proteinSummarization function.
Reached here in skyline
Reached here in skyline
Reached in maxq
Reached in maxq
Reached in maxq
Reached in prog
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getSummary1 +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getSummary1 +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getSummary1 +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getSummary2 +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "Number of PTMs" "Number of PTM Features"
[3] "Number of Features/PTM" "PTM Intensity Range"
[5] "Number of Unmod Proteins" "Number of Protein Peptides"
[7] "Number of Protein Features" "Number of Features/Peptide"
[9] "Number of Peptides/Protein" "Protein Intensity Range"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getSummary2 +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "Number of PTMs" "Number of PTM Features"
[3] "Number of Features/PTM" "PTM Intensity Range"
[5] "Number of Unmod Proteins" "Number of Protein Peptides"
[7] "Number of Protein Features" "Number of Features/Peptide"
[9] "Number of Peptides/Protein" "Protein Intensity Range"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getSummary2 +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
INFO [2023-10-15 23:11:20] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:20] ** Fractionation handled.
INFO [2023-10-15 23:11:20] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:20] ** Use all features that the dataset originally has.
INFO [2023-10-15 23:11:22] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:22] ** Fractionation handled.
INFO [2023-10-15 23:11:22] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:22] ** Use all features that the dataset originally has.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
INFO [2023-10-15 23:11:22] ** MSstatsTMT - proteinSummarization function
INFO [2023-10-15 23:11:22] ** Use all features that the dataset originally has.
INFO [2023-10-15 23:11:23] ** Use all features that the dataset originally has.
INFO [2023-10-15 23:11:24] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
INFO [2023-10-15 23:11:24] ** MSstatsTMT - proteinSummarization function
INFO [2023-10-15 23:11:24] ** Use all features that the dataset originally has.
INFO [2023-10-15 23:11:25] ** Use all features that the dataset originally has.
INFO [2023-10-15 23:11:27] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
INFO [2023-10-15 23:11:27] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:27] ** Fractionation handled.
INFO [2023-10-15 23:11:27] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:27] ** Use all features that the dataset originally has.
[1] "+++++++++ In Data Comparison +++++++++"
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
INFO [2023-10-15 23:11:27] ** MSstatsTMT - proteinSummarization function
INFO [2023-10-15 23:11:27] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
INFO [2023-10-15 23:11:27] ** MSstatsTMT - proteinSummarization function
INFO [2023-10-15 23:11:27] ** 'Norm' information in Condition is required for normalization. Please check it. At this moment, normalization is not performed.
INFO [2023-10-15 23:11:27] Design: 2 mixtures.
INFO [2023-10-15 23:11:27] Design: 1 MS run per mixture.
INFO [2023-10-15 23:11:27] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-10-15 23:11:27] Model fitting for 90 proteins.
|
| | 0%
|
|= | 1%
|
|== | 2%
|
|== | 3%
|
|=== | 4%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|======= | 10%
|
|======== | 11%
|
|========= | 12%
|
|========= | 13%
|
|========== | 14%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 21%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 31%
|
|======================= | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 39%
|
|============================ | 40%
|
|============================= | 41%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|===================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 56%
|
|======================================== | 57%
|
|======================================== | 58%
|
|========================================= | 59%
|
|========================================== | 60%
|
|=========================================== | 61%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|=============================================== | 68%
|
|================================================ | 69%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|====================================================== | 77%
|
|====================================================== | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 91%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
INFO [2023-10-15 23:11:30] Design: 2 mixtures.
INFO [2023-10-15 23:11:30] Design: 1 MS run per mixture.
INFO [2023-10-15 23:11:30] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2023-10-15 23:11:30] Model fitting for 85 proteins.
|
| | 0%
|
|= | 1%
|
|== | 2%
|
|== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|====== | 8%
|
|======= | 9%
|
|======= | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|=========== | 15%
|
|============ | 16%
|
|============ | 18%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 21%
|
|================ | 22%
|
|================ | 24%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|==================== | 28%
|
|===================== | 29%
|
|===================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 35%
|
|========================== | 36%
|
|========================== | 38%
|
|=========================== | 39%
|
|============================ | 40%
|
|============================= | 41%
|
|============================== | 42%
|
|============================== | 44%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================== | 48%
|
|=================================== | 49%
|
|=================================== | 51%
|
|==================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================== | 56%
|
|======================================== | 58%
|
|========================================= | 59%
|
|========================================== | 60%
|
|=========================================== | 61%
|
|============================================ | 62%
|
|============================================ | 64%
|
|============================================= | 65%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 69%
|
|================================================= | 71%
|
|================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|====================================================== | 76%
|
|====================================================== | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================== | 82%
|
|========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|=============================================================== | 89%
|
|=============================================================== | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|=================================================================== | 95%
|
|==================================================================== | 96%
|
|==================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
[1] "+++++++++ In Data Comparison +++++++++"
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
INFO [2023-10-15 23:11:34] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:34] ** Fractionation handled.
INFO [2023-10-15 23:11:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:35] ** Use all features that the dataset originally has.
INFO [2023-10-15 23:11:36] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:36] ** Fractionation handled.
INFO [2023-10-15 23:11:36] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:36] ** Use all features that the dataset originally has.
|
| | 0%
|
| | 0%[1] "+++++++++ In Data Comparison +++++++++"
[1] "+++++++++ In preprocessData +++++++++"
[1] "+++++++++ In getData +++++++++"
Reached in evidence
Reached in proteins_group
Reached in maxq annot
Reached in ump annot
Reached in ump annot
Reached in unmod
Reached in get_data
File type is sample
INFO [2023-10-15 23:11:40] ** Features with one or two measurements across runs are removed.
INFO [2023-10-15 23:11:40] ** Fractionation handled.
INFO [2023-10-15 23:11:40] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-10-15 23:11:40] ** Use all features that the dataset originally has.
|
| | 0%[ FAIL 0 | WARN 0 | SKIP 0 | PASS 114 ]
>
> proc.time()
user system elapsed
30.070 0.757 29.542
MSstatsShiny.Rcheck/MSstatsShiny-Ex.timings
| name | user | system | elapsed | |
| QC_check | 0.000 | 0.000 | 0.001 | |
| annotation.mine | 0.000 | 0.005 | 0.006 | |
| annotation.mq | 0.003 | 0.001 | 0.004 | |
| annotation.pd | 0.003 | 0.000 | 0.003 | |
| apply_adj | 4.673 | 0.148 | 4.813 | |
| dia_skyline_model | 0.038 | 0.032 | 0.070 | |
| dia_skyline_summarized | 0.331 | 0.676 | 1.007 | |
| evidence | 0.033 | 0.007 | 0.041 | |
| example_dia_skyline | 0.175 | 0.008 | 0.184 | |
| example_skyline_annotation | 0.002 | 0.000 | 0.002 | |
| groupComparisonPlots2 | 0.816 | 0.059 | 0.876 | |
| launch_MSstatsShiny | 0 | 0 | 0 | |
| lf_model | 0.206 | 0.000 | 0.206 | |
| lf_summarization_loop | 3.445 | 0.727 | 3.611 | |
| proteinGroups | 0.053 | 0.024 | 0.076 | |
| radioTooltip | 0.005 | 0.000 | 0.005 | |
| raw.mine | 0.141 | 0.004 | 0.145 | |
| raw.om | 0.047 | 0.000 | 0.046 | |
| raw.pd | 0.053 | 0.004 | 0.057 | |
| tmt_model | 6.901 | 0.192 | 6.176 | |
| tmt_pd_model | 0.083 | 0.008 | 0.090 | |
| tmt_pd_summarized | 0.426 | 0.736 | 1.162 | |
| tmt_summarization_loop | 5.018 | 0.044 | 4.144 | |
| uiObject | 0.000 | 0.004 | 0.000 | |
| xy_str | 0 | 0 | 0 | |