Devon Kohler
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/MSstatsLiP |
| git_branch: RELEASE_3_16 |
| git_last_commit: 48bf904 |
| git_last_commit_date: 2022-12-06 09:12:50 -0400 (Tue, 06 Dec 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:42 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the MSstatsLiP package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1285/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsLiP 1.4.1 (landing page) Devon Kohler
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSstatsLiP |
| Version: 1.4.1 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MSstatsLiP_1.4.1.tar.gz |
| StartedAt: 2023-04-11 03:43:42 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 03:47:40 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 237.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsLiP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MSstatsLiP.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MSstatsLiP_1.4.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MSstatsLiP.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MSstatsLiP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSstatsLiP' version '1.4.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MSstatsLiP' 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/MSstatsLiP/libs/x64/MSstatsLiP.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataProcessPlotsLiP 26.73 0.48 28.01
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'tinytest.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
'F:/biocbuild/bbs-3.16-bioc/meat/MSstatsLiP.Rcheck/00check.log'
for details.
MSstatsLiP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MSstatsLiP ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library' * installing *source* package 'MSstatsLiP' ... ** using staged installation ** libs g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++14 -shared -s -static-libgcc -o MSstatsLiP.dll tmp.def RcppExports.o model_adjustment.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-MSstatsLiP/00new/MSstatsLiP/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsLiP)
MSstatsLiP.Rcheck/tests/tinytest.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("MSstatsLiP")
+ }
test_SkylinetoMSstatsLiPFormat.R 0 tests
test_SkylinetoMSstatsLiPFormat.R 1 tests [0;32mOK[0m
test_SkylinetoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
test_SkylinetoMSstatsLiPFormat.R 3 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 4 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 5 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 6 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 7 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 8 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 9 tests [0;32mOK[0m INFO [2023-04-11 03:46:43] ** Raw data from Skyline imported successfully.
INFO [2023-04-11 03:46:43] ** Raw data from Skyline cleaned successfully.
INFO [2023-04-11 03:46:43] ** Using annotation extracted from quantification data.
test_SkylinetoMSstatsLiPFormat.R 10 tests [0;32mOK[0m [0;34m0.5s[0m
test_SpectronauttoMSstatsLiPFormat.R 0 tests
test_SpectronauttoMSstatsLiPFormat.R 0 tests
test_SpectronauttoMSstatsLiPFormat.R 1 tests [0;32mOK[0m
test_SpectronauttoMSstatsLiPFormat.R 2 tests [0;32mOK[0m INFO [2023-04-11 03:46:44] ** Raw data from Spectronaut imported successfully.
INFO [2023-04-11 03:46:44] ** Raw data from Spectronaut cleaned successfully.
INFO [2023-04-11 03:46:44] ** Using annotation extracted from quantification data.
INFO [2023-04-11 03:46:44] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2023-04-11 03:46:44] ** 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 [2023-04-11 03:46:44] ** PGQvalue not found in input columns.
INFO [2023-04-11 03:46:44] ** Intensities with values not smaller than 0.01 in EGQvalue are replaced with 0
INFO [2023-04-11 03:46:44] ** Features with all missing measurements across runs are removed.
INFO [2023-04-11 03:46:44] ** Shared peptides are removed.
INFO [2023-04-11 03:46:44] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2023-04-11 03:46:44] ** Features with one or two measurements across runs are removed.
INFO [2023-04-11 03:46:44] ** Run annotation merged with quantification data.
INFO [2023-04-11 03:46:44] ** Features with one or two measurements across runs are removed.
INFO [2023-04-11 03:46:44] ** Fractionation handled.
INFO [2023-04-11 03:46:44] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2023-04-11 03:46:44] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
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 [2023-04-11 03:46:44] ** Raw data from Spectronaut imported successfully.
INFO [2023-04-11 03:46:44] ** Raw data from Spectronaut cleaned successfully.
INFO [2023-04-11 03:46:44] ** Using annotation extracted from quantification data.
INFO [2023-04-11 03:46:44] ** 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;34m0.8s[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;34m26.8s[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;34m0.2s[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 [2023-04-11 03:47:11] == Start to test and get inference in whole plot ...
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INFO [2023-04-11 03:47:11] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2023-04-11 03:47:11] == Start to test and get inference in whole plot ...
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INFO [2023-04-11 03:47:11] == 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;34m0.7s[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;34m5.9s[0m
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;34m8.3s[0m
All ok, 111 results (43.2s)
Warning messages:
1: In max(datafeature.ptm$ABUNDANCE, na.rm = TRUE) :
no non-missing arguments to max; returning -Inf
2: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 1 has 0 rows but longest item has 1; filled with NA
3: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 3 has 0 rows but longest item has 1; filled with NA
4: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 4 has 0 rows but longest item has 1; filled with NA
5: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 1 has 0 rows but longest item has 1; filled with NA
6: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 2 has 0 rows but longest item has 1; filled with NA
7: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 3 has 0 rows but longest item has 1; filled with NA
8: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 1 has 0 rows but longest item has 1; filled with NA
9: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 2 has 0 rows but longest item has 1; filled with NA
10: In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
Item 3 has 0 rows but longest item has 1; filled with NA
>
> proc.time()
user system elapsed
48.68 1.29 50.01
MSstatsLiP.Rcheck/MSstatsLiP-Ex.timings
| name | user | system | elapsed | |
| LiPRawData | 0.04 | 0.00 | 0.03 | |
| MSstatsLiP_Summarized | 0.01 | 0.00 | 0.02 | |
| MSstatsLiP_data | 0.02 | 0.00 | 0.01 | |
| MSstatsLiP_model | 0 | 0 | 0 | |
| PCAPlotLiP | 1.70 | 0.09 | 1.80 | |
| ResistanceBarcodePlotLiP | 0 | 0 | 0 | |
| SkylineTest | 0.02 | 0.00 | 0.01 | |
| SkylinetoMSstatsLiPFormat | 0 | 0 | 0 | |
| SpectronauttoMSstatsLiPFormat | 0.70 | 0.02 | 0.72 | |
| StructuralBarcodePlotLiP | 2.97 | 0.05 | 3.02 | |
| TrPRawData | 0.00 | 0.01 | 0.01 | |
| annotSite | 0 | 0 | 0 | |
| calculateProteolyticResistance | 0.01 | 0.00 | 0.02 | |
| calculateTrypticity | 0.02 | 0.00 | 0.02 | |
| correlationPlotLiP | 0.33 | 0.00 | 0.33 | |
| dataProcessPlotsLiP | 26.73 | 0.48 | 28.01 | |
| dataSummarizationLiP | 0.69 | 0.02 | 0.71 | |
| groupComparisonLiP | 0.48 | 0.00 | 0.48 | |
| groupComparisonPlotsLiP | 1.91 | 0.05 | 1.95 | |
| locateMod | 0 | 0 | 0 | |
| locatePTM | 0.09 | 0.00 | 0.10 | |
| raw_lip | 0.07 | 0.00 | 0.06 | |
| raw_prot | 0.04 | 0.00 | 0.05 | |
| tidyFasta | 0.03 | 0.00 | 0.03 | |
| trypticHistogramLiP | 0.30 | 0.01 | 0.31 | |