Devon Kohler
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/MSstatsPTM |
| git_branch: RELEASE_3_18 |
| git_last_commit: 3844aca |
| git_last_commit_date: 2024-02-13 09:08:14 -0400 (Tue, 13 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:09 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1347/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsPTM 2.4.4 (landing page) Devon Kohler
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the MSstatsPTM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsPTM.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MSstatsPTM |
| Version: 2.4.4 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsPTM_2.4.4.tar.gz |
| StartedAt: 2024-04-16 01:18:48 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 01:23:28 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 280.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsPTM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MSstatsPTM_2.4.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ version ‘2.4.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsPTM’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘MSstats:::.getMedianSigmaSubject’ ‘MSstats:::.getVarComponent’
‘MSstatsConvert:::.filterFewMeasurements’
‘MSstatsConvert:::.filterManyColumns’
‘MSstatsConvert:::.getChannelColumns’
‘MSstatsConvert:::.standardizeColnames’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extract_pd_mods: no visible binding for global variable
‘..sequence_col’
.format.data.process.plots: no visible binding for global variable
‘ABUNDANCE’
.pivotPS: no visible binding for global variable ‘..keep_cols’
.plot.model.volcano: no visible binding for global variable
‘text.angle’
.progensis.add.sites: no visible binding for global variable
‘..col_order’
.qc.all.plot.lf: no visible binding for global variable ‘text.angle’
.qc.single.plot.lf: no visible binding for global variable ‘text.angle’
.removeCutoffSites: no visible binding for global variable
‘..mod_pep_col’
.rmConfounded: no visible binding for global variable ‘..col_res’
DIANNtoMSstatsPTMFormat: no visible binding for global variable
‘..protein_id_col’
FragPipetoMSstatsPTMFormat: no visible binding for global variable
‘..msstats_cols’
MSstatsPTMSiteLocator: no visible binding for global variable
‘..mod_pep_col’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘TMT.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘ptm.keyword’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘mod.num’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘which.proteinid.ptm’
MaxQtoMSstatsPTMFormat: no visible binding for global variable
‘PeptideSequence’
PStoMSstatsPTMFormat: no visible binding for global variable
‘Intensity’
ProgenesistoMSstatsPTMFormat: no visible binding for global variable
‘Type’
SkylinetoMSstatsPTMFormat: no visible binding for global variable
‘annotation_prot’
dataProcessPlotsPTM: no visible binding for global variable
‘PROTEINNAME’
dataProcessPlotsPTM: no visible binding for global variable
‘GLOBALPROTEIN’
dataSummarizationPTM: no visible binding for global variable ‘address’
locatePTM: no visible binding for global variable ‘..col_seq’
locatePTM: no visible binding for global variable ‘..col_fasta’
Undefined global functions or variables:
..col_fasta ..col_order ..col_res ..col_seq ..keep_cols ..mod_pep_col
..msstats_cols ..protein_id_col ..sequence_col ABUNDANCE
GLOBALPROTEIN Intensity PROTEINNAME PeptideSequence TMT.keyword Type
address annotation_prot mod.num ptm.keyword text.angle
which.proteinid.ptm
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
groupComparisonPlotsPTM 11.24 0.104 11.334
* 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 ...
‘MSstatsPTM_LabelFree_Workflow.Rmd’ using ‘UTF-8’... OK
‘MSstatsPTM_TMT_Workflow.Rmd’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/MSstatsPTM.Rcheck/00check.log’
for details.
MSstatsPTM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MSstatsPTM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘MSstatsPTM’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c model_adjustment.cpp -o model_adjustment.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o MSstatsPTM.so RcppExports.o model_adjustment.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-MSstatsPTM/00new/MSstatsPTM/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsPTM)
MSstatsPTM.Rcheck/tests/tinytest.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("MSstatsPTM")
+ }
test_converters.R............. 0 tests
test_converters.R............. 0 tests
test_converters.R............. 1 tests [0;32mOK[0m
test_converters.R............. 2 tests [0;32mOK[0m
test_converters.R............. 3 tests [0;32mOK[0m
test_converters.R............. 4 tests [0;32mOK[0m
test_converters.R............. 5 tests [0;32mOK[0m
test_converters.R............. 5 tests [0;32mOK[0m
test_converters.R............. 5 tests [0;32mOK[0m
test_converters.R............. 6 tests [0;32mOK[0m
test_converters.R............. 7 tests [0;32mOK[0m
test_converters.R............. 8 tests [0;32mOK[0m
test_converters.R............. 9 tests [0;32mOK[0m
test_converters.R............. 10 tests [0;32mOK[0m
test_converters.R............. 10 tests [0;32mOK[0m
test_converters.R............. 10 tests [0;32mOK[0m
test_converters.R............. 11 tests [0;32mOK[0m
test_converters.R............. 12 tests [0;32mOK[0m
test_converters.R............. 13 tests [0;32mOK[0m
test_converters.R............. 14 tests [0;32mOK[0m
test_converters.R............. 14 tests [0;32mOK[0m
test_converters.R............. 14 tests [0;32mOK[0m
test_converters.R............. 14 tests [0;32mOK[0m INFO [2024-04-16 01:21:33] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-04-16 01:21:33] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-04-16 01:21:33] ** Using provided annotation.
INFO [2024-04-16 01:21:33] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-04-16 01:21:33] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-04-16 01:21:33] ** Features with all missing measurements across runs are removed.
INFO [2024-04-16 01:21:33] ** Shared peptides are removed.
INFO [2024-04-16 01:21:33] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-04-16 01:21:33] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:33] ** Run annotation merged with quantification data.
INFO [2024-04-16 01:21:33] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:33] ** Fractionation handled.
INFO [2024-04-16 01:21:33] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-04-16 01:21:33] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 15 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-04-16 01:21:34] ** Using provided annotation.
INFO [2024-04-16 01:21:34] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-04-16 01:21:34] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-04-16 01:21:34] ** Features with all missing measurements across runs are removed.
INFO [2024-04-16 01:21:34] ** Shared peptides are removed.
INFO [2024-04-16 01:21:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:34] ** Run annotation merged with quantification data.
INFO [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:34] ** Fractionation handled.
INFO [2024-04-16 01:21:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-04-16 01:21:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 16 tests [0;32mOK[0m INFO: Extracting modifications
INFO [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-04-16 01:21:34] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-04-16 01:21:34] ** Using provided annotation.
INFO [2024-04-16 01:21:34] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-04-16 01:21:34] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-04-16 01:21:34] ** Features with all missing measurements across runs are removed.
INFO [2024-04-16 01:21:34] ** Shared peptides are removed.
INFO [2024-04-16 01:21:34] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:34] ** Run annotation merged with quantification data.
INFO [2024-04-16 01:21:34] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:34] ** Fractionation handled.
INFO [2024-04-16 01:21:34] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-04-16 01:21:34] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 17 tests [0;32mOK[0m INFO [2024-04-16 01:21:35] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-04-16 01:21:35] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-04-16 01:21:35] ** Using provided annotation.
INFO [2024-04-16 01:21:35] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-04-16 01:21:35] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-04-16 01:21:35] ** Features with all missing measurements across runs are removed.
INFO [2024-04-16 01:21:35] ** Shared peptides are removed.
INFO [2024-04-16 01:21:35] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-04-16 01:21:35] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:35] ** Run annotation merged with quantification data.
INFO [2024-04-16 01:21:35] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:35] ** Fractionation handled.
INFO [2024-04-16 01:21:35] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-04-16 01:21:35] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 18 tests [0;32mOK[0m
test_converters.R............. 19 tests [0;32mOK[0m INFO [2024-04-16 01:21:36] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-04-16 01:21:36] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-04-16 01:21:36] ** Using provided annotation.
INFO [2024-04-16 01:21:36] ** Run labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-04-16 01:21:36] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements across runs will be removed.
INFO [2024-04-16 01:21:36] ** Features with all missing measurements across runs are removed.
INFO [2024-04-16 01:21:36] ** Shared peptides are removed.
INFO [2024-04-16 01:21:36] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO [2024-04-16 01:21:36] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:36] ** Run annotation merged with quantification data.
INFO [2024-04-16 01:21:36] ** Features with one or two measurements across runs are removed.
INFO [2024-04-16 01:21:36] ** Fractionation handled.
INFO [2024-04-16 01:21:36] ** Updated quantification data to make balanced design. Missing values are marked by NA
INFO [2024-04-16 01:21:36] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
test_converters.R............. 20 tests [0;32mOK[0m
test_converters.R............. 21 tests [0;32mOK[0m
test_converters.R............. 22 tests [0;32mOK[0m [0;34m7.4s[0m
test_dataSummarizationPTM.R... 0 tests
test_dataSummarizationPTM.R... 1 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 2 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 3 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 4 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 5 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 6 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 7 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 8 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 9 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 10 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 11 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 12 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 13 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 14 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 15 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 16 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 17 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 18 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 19 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 20 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 21 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 22 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 23 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 24 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 25 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 26 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 27 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 28 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 29 tests [0;32mOK[0m
test_dataSummarizationPTM.R... 30 tests [0;32mOK[0m Starting PTM summarization...
test_dataSummarizationPTM.R... 31 tests [0;32mOK[0m [0;34m0.2s[0m
test_dataSummarizationPTM_TMT.R 0 tests
test_dataSummarizationPTM_TMT.R 1 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 2 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 3 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 4 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 5 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 6 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 7 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 8 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 9 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 10 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 11 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 12 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 13 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 14 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 15 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 16 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 17 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 18 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 19 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 20 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 21 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 22 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 23 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 24 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 25 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 26 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 27 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 28 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 29 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 30 tests [0;32mOK[0m
test_dataSummarizationPTM_TMT.R 31 tests [0;32mOK[0m [0;34m0.2s[0m
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 0 tests
test_groupComparisonPTM.R..... 1 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 2 tests [0;32mOK[0m Starting PTM modeling...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m Starting PTM modeling...
INFO [2024-04-16 01:21:40] == Start to test and get inference in whole plot ...
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 40%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|==================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================= | 56%
|
|======================================== | 57%
|
|======================================== | 58%
|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 60%
|
|=========================================== | 61%
|
|=========================================== | 62%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================= | 65%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================ | 69%
|
|================================================= | 70%
|
|================================================== | 71%
|
|================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 77%
|
|====================================================== | 78%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================= | 82%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
INFO [2024-04-16 01:21:43] == Comparisons for all proteins are done.
Starting Protein modeling...
INFO [2024-04-16 01:21:43] == Start to test and get inference in whole plot ...
|
| | 0%
|
|=== | 4%
|
|===== | 8%
|
|======== | 12%
|
|=========== | 15%
|
|============= | 19%
|
|================ | 23%
|
|=================== | 27%
|
|====================== | 31%
|
|======================== | 35%
|
|=========================== | 38%
|
|============================== | 42%
|
|================================ | 46%
|
|=================================== | 50%
|
|====================================== | 54%
|
|======================================== | 58%
|
|=========================================== | 62%
|
|============================================== | 65%
|
|================================================ | 69%
|
|=================================================== | 73%
|
|====================================================== | 77%
|
|========================================================= | 81%
|
|=========================================================== | 85%
|
|============================================================== | 88%
|
|================================================================= | 92%
|
|=================================================================== | 96%
|
|======================================================================| 100%
INFO [2024-04-16 01:21:44] == Comparisons for all proteins are done.
Starting adjustment...
test_groupComparisonPTM.R..... 3 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 4 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 5 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 6 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 7 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 8 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 9 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m Starting PTM modeling...
INFO [2024-04-16 01:21:44] Design: 2 mixtures.
INFO [2024-04-16 01:21:44] Design: 1 MS run per mixture.
INFO [2024-04-16 01:21:44] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2024-04-16 01:21:44] 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 [2024-04-16 01:21:46] Testing 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%
Starting Protein modeling...
INFO [2024-04-16 01:21:47] Design: 2 mixtures.
INFO [2024-04-16 01:21:47] Design: 1 MS run per mixture.
INFO [2024-04-16 01:21:47] Design: group comparison design (Different conditions contains different biological subjects).
INFO [2024-04-16 01:21:47] 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%
INFO [2024-04-16 01:21:51] Testing 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%
Starting adjustment...
test_groupComparisonPTM.R..... 10 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 11 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 12 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 13 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 14 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 15 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 16 tests [0;32mOK[0m
test_groupComparisonPTM.R..... 17 tests [0;32mOK[0m [0;34m15.4s[0m
All ok, 101 results (23.2s)
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
29.228 0.809 29.112
MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings
| name | user | system | elapsed | |
| DIANNtoMSstatsPTMFormat | 0.001 | 0.000 | 0.000 | |
| FragPipetoMSstatsPTMFormat | 0.476 | 0.044 | 0.455 | |
| MSstatsPTMSiteLocator | 0 | 0 | 0 | |
| MaxQtoMSstatsPTMFormat | 0.858 | 0.040 | 0.820 | |
| PDtoMSstatsPTMFormat | 0.761 | 0.060 | 0.763 | |
| PStoMSstatsPTMFormat | 0.069 | 0.000 | 0.069 | |
| ProgenesistoMSstatsPTMFormat | 0.047 | 0.000 | 0.047 | |
| SkylinetoMSstatsPTMFormat | 0.047 | 0.000 | 0.047 | |
| SpectronauttoMSstatsPTMFormat | 0.599 | 0.035 | 0.552 | |
| annotSite | 0.001 | 0.000 | 0.000 | |
| dataProcessPlotsPTM | 2.114 | 0.037 | 2.109 | |
| dataSummarizationPTM | 2.272 | 0.012 | 2.133 | |
| dataSummarizationPTM_TMT | 4.619 | 0.120 | 4.200 | |
| designSampleSizePTM | 4.483 | 0.056 | 4.534 | |
| fragpipe_annotation | 0.002 | 0.000 | 0.002 | |
| fragpipe_annotation_protein | 0.002 | 0.000 | 0.002 | |
| fragpipe_input | 0.004 | 0.000 | 0.004 | |
| fragpipe_input_protein | 0.004 | 0.000 | 0.004 | |
| groupComparisonPTM | 3.903 | 0.064 | 3.958 | |
| groupComparisonPlotsPTM | 11.240 | 0.104 | 11.334 | |
| locateMod | 0.001 | 0.000 | 0.000 | |
| locatePTM | 0.014 | 0.000 | 0.014 | |
| maxq_lf_annotation | 0.001 | 0.000 | 0.002 | |
| maxq_lf_evidence | 0.008 | 0.000 | 0.008 | |
| maxq_tmt_annotation | 0.001 | 0.000 | 0.001 | |
| maxq_tmt_evidence | 0.009 | 0.004 | 0.012 | |
| pd_annotation | 0.001 | 0.000 | 0.001 | |
| pd_psm_input | 0.008 | 0.000 | 0.008 | |
| pd_testing_output | 0.068 | 0.048 | 0.116 | |
| raw.input | 0.065 | 0.000 | 0.065 | |
| raw.input.tmt | 0.005 | 0.000 | 0.005 | |
| spectronaut_annotation | 0.001 | 0.000 | 0.002 | |
| spectronaut_input | 0.004 | 0.000 | 0.004 | |
| summary.data | 0.15 | 0.12 | 0.27 | |
| summary.data.tmt | 0.320 | 0.208 | 0.528 | |
| tidyFasta | 0.01 | 0.00 | 0.01 | |