Devon Kohler
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MSstatsLiP |
| git_branch: devel |
| git_last_commit: 256206e |
| git_last_commit_date: 2024-10-29 11:05:42 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1347/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsLiP 1.13.0 (landing page) Devon Kohler
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the MSstatsLiP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsLiP.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: MSstatsLiP |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsLiP_1.13.0.tar.gz |
| StartedAt: 2024-12-23 20:22:46 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 20:24:01 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 74.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsLiP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsLiP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsLiP_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsLiP.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘MSstatsLiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsLiP’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsLiP’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ResistanceBarcodePlotLiP: no visible binding for global variable
‘GROUP’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘Protein’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘uniprot_iso’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘PeptideSequence’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘Accessibility_ratio’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘Index’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘Label’
ResistanceBarcodePlotLiP: no visible binding for global variable ‘sig’
ResistanceBarcodePlotLiP: no visible binding for global variable
‘Coverage’
StructuralBarcodePlotLiP: no visible binding for global variable
‘NSEMI_TRI’
StructuralBarcodePlotLiP: no visible binding for global variable
‘CSEMI_TRI’
calculateProteolyticResistance: no visible binding for global variable
‘LogIntensities’
calculateProteolyticResistance: no visible binding for global variable
‘Protein.y’
Undefined global functions or variables:
Accessibility_ratio CSEMI_TRI Coverage GROUP Index Label
LogIntensities NSEMI_TRI PeptideSequence Protein Protein.y sig
uniprot_iso
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataProcessPlotsLiP 6.62 0.044 6.758
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/MSstatsLiP.Rcheck/00check.log’
for details.
MSstatsLiP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsLiP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘MSstatsLiP’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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 MSstatsLiP.so RcppExports.o model_adjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-MSstatsLiP/00new/MSstatsLiP/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 (MSstatsLiP)
MSstatsLiP.Rcheck/tests/tinytest.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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("MSstatsLiP")
+ }
test_SkylinetoMSstatsLiPFormat.R 0 tests FUNCTION DEPRECATION NOTICE: We would like to notify you that the SkylinetoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SkylinetoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SkylinetoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
FUNCTION DEPRECATION NOTICE: We would like to notify you that the SkylinetoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SkylinetoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SkylinetoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
test_SkylinetoMSstatsLiPFormat.R 1 tests [0;32mOK[0m FUNCTION DEPRECATION NOTICE: We would like to notify you that the SkylinetoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SkylinetoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SkylinetoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
test_SkylinetoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
test_SkylinetoMSstatsLiPFormat.R 3 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:44] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 4 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:44] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 5 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:44] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 6 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:44] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 7 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:44] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 8 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:44] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:44] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 9 tests [0;32mOK[0m INFO [2024-12-23 20:23:44] ** Raw data from Skyline imported successfully.
INFO [2024-12-23 20:23:45] ** Raw data from Skyline cleaned successfully.
INFO [2024-12-23 20:23:45] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 10 tests [0;32mOK[0m [0;34m0.1s[0m
test_SpectronauttoMSstatsLiPFormat.R 0 tests
test_SpectronauttoMSstatsLiPFormat.R 0 tests FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
test_SpectronauttoMSstatsLiPFormat.R 1 tests [0;32mOK[0m FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
test_SpectronauttoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2024-12-23 20:23:45] ** Raw data from Spectronaut imported successfully.
INFO [2024-12-23 20:23:45] ** Raw data from Spectronaut cleaned successfully.
INFO [2024-12-23 20:23:45] ** Using annotation extracted from quantification data.
INFO [2024-12-23 20:23:45] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-23 20:23:45] ** 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 [2024-12-23 20:23:45] ** PGQvalue not found in input columns.
INFO [2024-12-23 20:23:45] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO [2024-12-23 20:23:45] ** Features with all missing measurements across runs are removed.
INFO [2024-12-23 20:23:45] ** Shared peptides are removed.
INFO [2024-12-23 20:23:45] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-12-23 20:23:45] ** Features with one or two measurements across runs are removed.
INFO [2024-12-23 20:23:45] ** Run annotation merged with quantification data.
INFO [2024-12-23 20:23:45] ** Features with one or two measurements across runs are removed.
INFO [2024-12-23 20:23:45] ** Fractionation handled.
INFO [2024-12-23 20:23:45] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-12-23 20:23:45] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
FUNCTION DEPRECATION NOTICE: We would like to notify you that the SpectronauttoMSstatsFormat function currently available in both MSstats and MSstatsConvert, will undergo a transition process. Starting from release 3.21 the SpectronauttoMSstatsFormat function in MSstats will be deprecated. Please take the necessary steps to update your codebase and migrate to MSstatsConvert::SpectronauttoMSstatsFormat before release 3.21 to avoid any disruptions to your workflow.
test_SpectronauttoMSstatsLiPFormat.R 3 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 4 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 5 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 6 tests [0;32mOK[0m INFO [2024-12-23 20:23:45] ** Raw data from Spectronaut imported successfully.
INFO [2024-12-23 20:23:45] ** Raw data from Spectronaut cleaned successfully.
INFO [2024-12-23 20:23:45] ** Using annotation extracted from quantification data.
INFO [2024-12-23 20:23:45] ** Run labels were standardized to remove symbols such as '.' or '%'.
test_SpectronauttoMSstatsLiPFormat.R 7 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 8 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 9 tests [0;32mOK[0m [0;34m0.4s[0m
test_dataProcessPlotsLiP.R.... 0 tests
test_dataProcessPlotsLiP.R.... 1 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 2 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 3 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 4 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 5 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 6 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 7 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 8 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 9 tests [0;32mOK[0m
test_dataProcessPlotsLiP.R.... 10 tests [0;32mOK[0m Drew the Profile plot for P14164_ILQNDLK (1 of 14)
Drew the Profile plot for P17891_ALQLINQDDADIIGGRDR (2 of 14)
Drew the Profile plot for P17891_DDDTDFLK (3 of 14)
Drew the Profile plot for P36112_SNDLLSGLTGSSQTR (4 of 14)
Drew the Profile plot for P38805_LGQTVGR (5 of 14)
Drew the Profile plot for P46959_DIIGKPYGSQIAIR (6 of 14)
Drew the Profile plot for P52893_SSSQGVEGIRK (7 of 14)
Drew the Profile plot for P52911_TWITEDDFEQIK (8 of 14)
Drew the Profile plot for P53235_ERQAVGDKLEDTQVLK (9 of 14)
Drew the Profile plot for P53858_FLDNHEVDSIVSLER (10 of 14)
Drew the Profile plot for Q02908_ISVISGVGVR (11 of 14)
Drew the Profile plot for Q12248_EFQSVSDLWK (12 of 14)
Drew the Profile plot for P16622_SHLQSNQLYSNQLPLDFALGK (13 of 14)
Drew the Profile plot for P24004_FIGASEQNIR (14 of 14)
Drew the Profile plot for P14164_ILQNDLK ( 1 of 14 )
Drew the Profile plot for P17891_ALQLINQDDADIIGGRDR ( 2 of 14 )
Drew the Profile plot for P17891_DDDTDFLK ( 3 of 14 )
Drew the Profile plot for P36112_SNDLLSGLTGSSQTR ( 4 of 14 )
Drew the Profile plot for P38805_LGQTVGR ( 5 of 14 )
Drew the Profile plot for P46959_DIIGKPYGSQIAIR ( 6 of 14 )
Drew the Profile plot for P52893_SSSQGVEGIRK ( 7 of 14 )
Drew the Profile plot for P52911_TWITEDDFEQIK ( 8 of 14 )
Drew the Profile plot for P53235_ERQAVGDKLEDTQVLK ( 9 of 14 )
Drew the Profile plot for P53858_FLDNHEVDSIVSLER ( 10 of 14 )
Drew the Profile plot for Q02908_ISVISGVGVR ( 11 of 14 )
Drew the Profile plot for Q12248_EFQSVSDLWK ( 12 of 14 )
Drew the Profile plot for P16622_SHLQSNQLYSNQLPLDFALGK ( 13 of 14 )
Drew the Profile plot for P24004_FIGASEQNIR ( 14 of 14 )
test_dataProcessPlotsLiP.R.... 11 tests [0;32mOK[0m Drew the Quality Contol plot(boxplot) for all ptms/proteins.
Drew the Quality Contol plot(boxplot) for P14164_ILQNDLK (1 of 14)
Drew the Quality Contol plot(boxplot) for P17891_ALQLINQDDADIIGGRDR (2 of 14)
Drew the Quality Contol plot(boxplot) for P17891_DDDTDFLK (3 of 14)
Drew the Quality Contol plot(boxplot) for P36112_SNDLLSGLTGSSQTR (4 of 14)
Drew the Quality Contol plot(boxplot) for P38805_LGQTVGR (5 of 14)
Drew the Quality Contol plot(boxplot) for P46959_DIIGKPYGSQIAIR (6 of 14)
Drew the Quality Contol plot(boxplot) for P52893_SSSQGVEGIRK (7 of 14)
Drew the Quality Contol plot(boxplot) for P52911_TWITEDDFEQIK (8 of 14)
Drew the Quality Contol plot(boxplot) for P53235_ERQAVGDKLEDTQVLK (9 of 14)
Drew the Quality Contol plot(boxplot) for P53858_FLDNHEVDSIVSLER (10 of 14)
Drew the Quality Contol plot(boxplot) for Q02908_ISVISGVGVR (11 of 14)
Drew the Quality Contol plot(boxplot) for Q12248_EFQSVSDLWK (12 of 14)
Drew the Quality Contol plot(boxplot) for P16622_SHLQSNQLYSNQLPLDFALGK (13 of 14)
Drew the Quality Contol plot(boxplot) for P24004_FIGASEQNIR (14 of 14)
test_dataProcessPlotsLiP.R.... 12 tests [0;32mOK[0m [0;34m7.2s[0m
test_dataSummarizationLiP.R... 0 tests
test_dataSummarizationLiP.R... 0 tests
test_dataSummarizationLiP.R... 1 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 2 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 3 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 4 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 5 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 6 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 7 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 8 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 9 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 10 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 11 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 12 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 13 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 14 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 15 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 16 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 17 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 18 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 19 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 20 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 21 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 22 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 23 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 24 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 25 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 26 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 27 tests [0;32mOK[0m
test_dataSummarizationLiP.R... 28 tests [0;32mOK[0m Starting PTM summarization...
test_dataSummarizationLiP.R... 29 tests [0;32mOK[0m [0;36m66ms[0m
test_groupComparisonLiP.R..... 0 tests
test_groupComparisonLiP.R..... 0 tests
test_groupComparisonLiP.R..... 1 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 2 tests [0;32mOK[0m Starting PTM modeling...
test_groupComparisonLiP.R..... 3 tests [0;32mOK[0m Starting PTM modeling...
INFO [2024-12-23 20:23:52] == Start to test and get inference in whole plot ...
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INFO [2024-12-23 20:23:52] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2024-12-23 20:23:52] == Start to test and get inference in whole plot ...
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INFO [2024-12-23 20:23:52] == Comparisons for all proteins are done.
Starting adjustment...
test_groupComparisonLiP.R..... 3 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 4 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 5 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 6 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 7 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 8 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 9 tests [0;32mOK[0m
test_groupComparisonLiP.R..... 10 tests [0;32mOK[0m [0;34m0.2s[0m
test_groupComparisonPlotsLiP.R 0 tests
test_groupComparisonPlotsLiP.R 1 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 2 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 3 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 4 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 5 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 6 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 7 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 8 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 9 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 10 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 11 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 12 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 13 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 14 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 15 tests [0;32mOK[0m
test_groupComparisonPlotsLiP.R 16 tests [0;32mOK[0m [0;34m1.3s[0m
test_trypticHistogramLiP.R.... 0 tests
test_trypticHistogramLiP.R.... 0 tests
test_trypticHistogramLiP.R.... 0 tests
test_trypticHistogramLiP.R.... 1 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 2 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 3 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 4 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 5 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 6 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 7 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 8 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 9 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 10 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 11 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 12 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 13 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 14 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 15 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 16 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 17 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 18 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 19 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 20 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 21 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 22 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 23 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 24 tests [0;32mOK[0m
test_trypticHistogramLiP.R.... 25 tests [0;32mOK[0m [0;34m3.0s[0m
All ok, 111 results (12.3s)
Warning message:
In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
>
> proc.time()
user system elapsed
13.840 0.238 14.604
MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsLiPFormat | 0.007 | 0.001 | 0.009 | |
| LiPRawData | 0.011 | 0.001 | 0.011 | |
| MSstatsLiP_Summarized | 0.005 | 0.001 | 0.005 | |
| MSstatsLiP_data | 0.002 | 0.000 | 0.002 | |
| MSstatsLiP_model | 0.003 | 0.001 | 0.004 | |
| PCAPlotLiP | 0.497 | 0.013 | 0.510 | |
| ResistanceBarcodePlotLiP | 0.000 | 0.000 | 0.001 | |
| SkylineTest | 0.002 | 0.000 | 0.003 | |
| SkylinetoMSstatsLiPFormat | 0.002 | 0.000 | 0.002 | |
| SpectronauttoMSstatsLiPFormat | 0.289 | 0.005 | 0.293 | |
| StructuralBarcodePlotLiP | 1.026 | 0.019 | 1.049 | |
| TrPRawData | 0.002 | 0.000 | 0.003 | |
| annotSite | 0 | 0 | 0 | |
| calculateProteolyticResistance | 0.003 | 0.000 | 0.002 | |
| calculateTrypticity | 0.004 | 0.001 | 0.004 | |
| correlationPlotLiP | 0.072 | 0.001 | 0.072 | |
| dataProcessPlotsLiP | 6.620 | 0.044 | 6.758 | |
| dataSummarizationLiP | 0.221 | 0.005 | 0.237 | |
| groupComparisonLiP | 0.420 | 0.008 | 0.442 | |
| groupComparisonPlotsLiP | 0.479 | 0.012 | 0.492 | |
| locateMod | 0.000 | 0.000 | 0.001 | |
| locatePTM | 0.022 | 0.001 | 0.029 | |
| raw_lip | 0.017 | 0.001 | 0.018 | |
| raw_prot | 0.020 | 0.001 | 0.022 | |
| tidyFasta | 0.007 | 0.001 | 0.007 | |
| trypticHistogramLiP | 0.082 | 0.001 | 0.087 | |