Devon Kohler
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/MSstatsTMT |
| git_branch: RELEASE_3_20 |
| git_last_commit: f5587c4 |
| git_last_commit_date: 2024-11-14 15:58:50 -0500 (Thu, 14 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1359/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsTMT 2.14.1 (landing page) Devon Kohler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the MSstatsTMT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsTMT.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: MSstatsTMT |
| Version: 2.14.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsTMT_2.14.1.tar.gz |
| StartedAt: 2024-12-20 06:38:27 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 06:43:24 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 297.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsTMT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsTMT_2.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘2.14.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MSstatsTMT’ 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 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
.checkRepeatedMeasures: no visible global function definition for ‘.’
.checkSingleSubject: no visible global function definition for ‘.’
.checkTechReplicate: no visible global function definition for ‘.’
.getGroupLabel: no visible binding for global variable ‘Condition’
.getVarComponentTMT : <anonymous>: no visible global function
definition for ‘is’
.handleSingleContrastTMT: no visible global function definition for
‘.mygrad’
.plotProfileTMT: no visible global function definition for ‘.’
.plotProfileTMT: no visible binding for global variable ‘censored’
.savePlotlyPlotHTML: no visible global function definition for ‘zip’
Undefined global functions or variables:
. .mygrad Condition censored is zip
Consider adding
importFrom("methods", "is")
importFrom("utils", "zip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'dot-documentFunction.Rd':
‘removeProtein_with1Peptide’ ‘use_log_file’ ‘append’ ‘verbose’
‘log_file_path’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataProcessPlotsTMT 68.764 0.784 71.740
groupComparisonTMT 11.531 0.336 13.634
designSampleSizeTMT 10.563 0.355 13.549
proteinSummarization 7.827 0.372 7.906
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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-3.20-bioc/meat/MSstatsTMT.Rcheck/00check.log’
for details.
MSstatsTMT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsTMT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MSstatsTMT’ ... ** using staged installation ** 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 (MSstatsTMT)
MSstatsTMT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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.
> library(testthat)
> library(MSstatsTMT)
>
> test_check("MSstatsTMT")
INFO [2024-12-20 06:42:53] ** Raw data from ProteomeDiscoverer imported successfully.
INFO [2024-12-20 06:42:53] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO [2024-12-20 06:42:53] ** Using provided annotation.
INFO [2024-12-20 06:42:54] ** Raw data from MaxQuant imported successfully.
INFO [2024-12-20 06:42:54] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-20 06:42:54] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-20 06:42:54] ** Rows with values of Potentialcontaminant equal to + are removed
INFO [2024-12-20 06:42:54] ** Rows with values of Reverse equal to + are removed
INFO [2024-12-20 06:42:54] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO [2024-12-20 06:42:54] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-20 06:42:54] ** Raw data from MaxQuant cleaned successfully.
INFO [2024-12-20 06:42:54] ** Using provided annotation.
INFO [2024-12-20 06:42:54] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-20 06:42:54] ** The following options are used:
- Features will be defined by the columns: PeptideSequence, PrecursorCharge
- Shared peptides will be removed.
- Proteins with single feature will not be removed.
- Features with less than 3 measurements within each run will be removed.
INFO [2024-12-20 06:42:54] ** Features with all missing measurements across channels within each run are removed.
INFO [2024-12-20 06:42:54] ** Shared peptides are removed.
INFO [2024-12-20 06:42:54] ** Features with one or two measurements across channels within each run are removed.
INFO [2024-12-20 06:42:54] ** PSMs have been aggregated to peptide ions.
INFO [2024-12-20 06:42:54] ** Raw data from SpectroMine imported successfully.
INFO [2024-12-20 06:42:54] ** Raw data from SpectroMine cleaned successfully.
INFO [2024-12-20 06:42:54] ** Using provided annotation.
INFO [2024-12-20 06:42:54] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO [2024-12-20 06:42:54] Design: 5 mixtures.
INFO [2024-12-20 06:42:54] Design: 3 technical replicated MS runs per mixture.
INFO [2024-12-20 06:42:54] Design: 1 subject per condition (No biological variation).
INFO [2024-12-20 06:42:54] Model fitting for 10 proteins.
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INFO [2024-12-20 06:42:56] Testing for 10 proteins:
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INFO [2024-12-20 06:42:57] Design: 5 mixtures.
INFO [2024-12-20 06:42:57] Design: 3 technical replicated MS runs per mixture.
INFO [2024-12-20 06:42:57] Design: 1 subject per condition (No biological variation).
INFO [2024-12-20 06:42:57] Model fitting for 10 proteins.
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INFO [2024-12-20 06:42:59] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:42:59] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1 of 15 )
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INFO [2024-12-20 06:43:00] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw ( 2 of 15 )
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INFO [2024-12-20 06:43:00] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw ( 3 of 15 )
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INFO [2024-12-20 06:43:01] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw ( 4 of 15 )
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INFO [2024-12-20 06:43:01] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw ( 5 of 15 )
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INFO [2024-12-20 06:43:02] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01raw ( 6 of 15 )
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INFO [2024-12-20 06:43:02] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02raw ( 7 of 15 )
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INFO [2024-12-20 06:43:03] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01raw ( 8 of 15 )
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INFO [2024-12-20 06:43:03] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02raw ( 9 of 15 )
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INFO [2024-12-20 06:43:04] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01raw ( 10 of 15 )
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INFO [2024-12-20 06:43:04] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02raw ( 11 of 15 )
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INFO [2024-12-20 06:43:05] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03raw ( 12 of 15 )
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INFO [2024-12-20 06:43:05] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03raw ( 13 of 15 )
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INFO [2024-12-20 06:43:06] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw ( 14 of 15 )
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INFO [2024-12-20 06:43:06] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03raw ( 15 of 15 )
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INFO [2024-12-20 06:43:07] ** Protein-level summarization done by MSstats.
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:07] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:08] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:08] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:08] ** MSstatsTMT - proteinSummarization function
INFO [2024-12-20 06:43:08] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1 of 15 )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
>
> proc.time()
user system elapsed
21.583 1.154 22.057
MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings
| name | user | system | elapsed | |
| MaxQtoMSstatsTMTFormat | 1.194 | 0.194 | 1.597 | |
| OpenMStoMSstatsTMTFormat | 0.530 | 0.026 | 0.527 | |
| PDtoMSstatsTMTFormat | 3.403 | 0.224 | 3.617 | |
| SpectroMinetoMSstatsTMTFormat | 0.487 | 0.037 | 0.517 | |
| annotation.mine | 0.004 | 0.001 | 0.006 | |
| annotation.mq | 0.004 | 0.001 | 0.006 | |
| annotation.pd | 0.004 | 0.001 | 0.006 | |
| dataProcessPlotsTMT | 68.764 | 0.784 | 71.740 | |
| designSampleSizeTMT | 10.563 | 0.355 | 13.549 | |
| evidence | 0.058 | 0.015 | 0.090 | |
| groupComparisonTMT | 11.531 | 0.336 | 13.634 | |
| input.pd | 0.055 | 0.005 | 0.061 | |
| proteinGroups | 0.343 | 0.112 | 0.458 | |
| proteinSummarization | 7.827 | 0.372 | 7.906 | |
| quant.pd.msstats | 0.046 | 0.005 | 0.050 | |
| raw.mine | 0.014 | 0.004 | 0.018 | |
| raw.om | 0.007 | 0.002 | 0.009 | |
| raw.pd | 0.030 | 0.010 | 0.038 | |
| test.pairwise | 0.006 | 0.001 | 0.008 | |