Ting Huang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/MSstatsTMT |
| Branch: RELEASE_3_12 |
| Last Commit: 5c9e714 |
| Last Changed Date: 2020-12-20 23:47:37 -0400 (Sun, 20 Dec 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:35:51 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the MSstatsTMT package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1171/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsTMT 1.8.2 (landing page) Ting Huang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MSstatsTMT |
| Version: 1.8.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsTMT_1.8.2.tar.gz |
| StartedAt: 2021-05-06 04:01:35 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:04:37 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 182.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsTMT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsTMT_1.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘1.8.2’
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataProcessPlotsTMT 41.766 0.562 42.402
groupComparisonTMT 12.940 0.313 13.357
proteinSummarization 6.389 0.248 6.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MSstatsTMT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstatsTMT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.
> library(testthat)
> library(MSstatsTMT)
>
> test_check("MSstatsTMT")
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Summary of Features :
count
# of Protein 10
# of Peptides/Protein 4-29
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
count
# of Protein 10
# of Peptides/Protein 3-33
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Protein 10
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# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
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# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Protein 10
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# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
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# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
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# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
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# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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Summary of Samples :
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# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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Summary of Samples :
0.125 0.5 0.667 1 Norm
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# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Protein 10
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# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
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# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Protein 10
# of Peptides/Protein 3-31
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
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# of Protein 10
# of Peptides/Protein 1-31
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
count
# of Protein 10
# of Peptides/Protein 3-34
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
count
# of Protein 10
# of Peptides/Protein 2-30
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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Summary of Features :
count
# of Protein 10
# of Peptides/Protein 5-32
# of Transitions/Peptide 1-1
Summary of Samples :
0.125 0.5 0.667 1 Norm
# of MS runs 2 2 2 2 2
# of Biological Replicates 1 1 1 1 1
# of Technical Replicates 2 2 2 2 2
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
>
> proc.time()
user system elapsed
17.898 0.814 18.761
MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings
| name | user | system | elapsed | |
| MaxQtoMSstatsTMTFormat | 0.552 | 0.081 | 0.635 | |
| OpenMStoMSstatsTMTFormat | 0.494 | 0.015 | 0.509 | |
| PDtoMSstatsTMTFormat | 1.727 | 0.038 | 1.768 | |
| SpectroMinetoMSstatsTMTFormat | 0.614 | 0.030 | 0.644 | |
| annotation.mine | 0.003 | 0.000 | 0.003 | |
| annotation.mq | 0.004 | 0.001 | 0.006 | |
| annotation.pd | 0.004 | 0.001 | 0.006 | |
| dataProcessPlotsTMT | 41.766 | 0.562 | 42.402 | |
| evidence | 0.019 | 0.013 | 0.032 | |
| groupComparisonTMT | 12.940 | 0.313 | 13.357 | |
| input.pd | 0.012 | 0.001 | 0.014 | |
| proteinGroups | 0.093 | 0.035 | 0.129 | |
| proteinSummarization | 6.389 | 0.248 | 6.696 | |
| quant.pd.msstats | 0.003 | 0.000 | 0.004 | |
| raw.mine | 0.007 | 0.002 | 0.009 | |
| raw.om | 0.004 | 0.001 | 0.005 | |
| raw.pd | 0.007 | 0.003 | 0.009 | |
| test.pairwise | 0.003 | 0.000 | 0.003 | |