Ting Huang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MSstatsTMT |
| Branch: RELEASE_3_9 |
| Last Commit: c1382c3 |
| Last Changed Date: 2019-05-04 16:12:18 -0400 (Sat, 04 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:03:28 -0400 (Wed, 16 Oct 2019).
| Package 1061/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSstatsTMT 1.2.7 Ting Huang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MSstatsTMT |
| Version: 1.2.7 |
| 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_1.2.7.tar.gz |
| StartedAt: 2019-10-16 04:55:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:59:34 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 234.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsTMT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.2.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSstatsTMT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘1.2.7’
* 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 or elapsed time > 5s
user system elapsed
dataProcessPlotsTMT 61.043 2.303 60.178
groupComparisonTMT 13.499 1.750 12.540
proteinSummarization 11.465 1.351 10.036
* 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/3.6/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 Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’ ** testing if installed package keeps a record of temporary installation path * DONE (MSstatsTMT)
MSstatsTMT.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Warning message:
replacing previous import 'MASS::select' by 'dplyr::select' when loading 'MSstats'
>
> test_check("MSstatsTMT")
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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|======= | 10%
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|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
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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|======= | 10%
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|=============================================================== | 90%
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|======================================================================| 100%
Summary of Features :
count
# of Protein 10
# of Peptides/Protein 3-29
# 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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|=============================================================== | 90%
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|======================================================================| 100%
Summary of Features :
count
# of Protein 10
# of Peptides/Protein 1-28
# 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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|======================================================================| 100%
Summary of Features :
count
# of Protein 10
# of Peptides/Protein 1-30
# 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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|======================================================================| 100%
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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|======================================================================| 100%
Summary of Features :
count
# of Protein 10
# of Peptides/Protein 4-31
# 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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|======================================================================| 100%
Summary of Features :
count
# of Protein 10
# of Peptides/Protein 3-30
# 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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|======================================================================| 100%
Summary of Features :
count
# of Protein 10
# of Peptides/Protein 5-30
# 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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|======================================================== | 80%
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|=============================================================== | 90%
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|======================================================================| 100%
Summary of Features :
count
# 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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|=============================================================== | 90%
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|======================================================================| 100%
Summary of Features :
count
# 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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|======================================================================| 100%
Summary of Features :
count
# 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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|======================================================================| 100%
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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|=============================================================== | 90%
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|======================================================================| 100%
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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|=============================================================== | 90%
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|======================================================================| 100%
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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══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
21.433 2.632 20.721
MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings
| name | user | system | elapsed | |
| MaxQtoMSstatsTMTFormat | 1.896 | 0.922 | 1.100 | |
| PDtoMSstatsTMTFormat | 2.244 | 0.402 | 2.538 | |
| SpectroMinetoMSstatsTMTFormat | 0.952 | 0.302 | 0.902 | |
| annotation.mine | 0.017 | 0.013 | 0.006 | |
| annotation.mq | 0.016 | 0.013 | 0.006 | |
| annotation.pd | 0.015 | 0.011 | 0.006 | |
| dataProcessPlotsTMT | 61.043 | 2.303 | 60.178 | |
| evidence | 0.119 | 0.099 | 0.048 | |
| groupComparisonTMT | 13.499 | 1.750 | 12.540 | |
| input.pd | 0.016 | 0.005 | 0.019 | |
| proteinGroups | 0.729 | 0.512 | 0.289 | |
| proteinSummarization | 11.465 | 1.351 | 10.036 | |
| quant.pd.msstats | 0.020 | 0.013 | 0.007 | |
| raw.mine | 0.060 | 0.046 | 0.019 | |
| raw.pd | 0.076 | 0.064 | 0.025 | |
| test.pairwise | 0.014 | 0.011 | 0.005 | |