Ting Huang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/MSstatsTMT |
| Branch: RELEASE_3_11 |
| Last Commit: cbcd335 |
| Last Changed Date: 2020-10-13 12:31:10 -0400 (Tue, 13 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:13 -0400 (Sat, 17 Oct 2020).
| 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 1148/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MSstatsTMT 1.6.6 Ting Huang
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: MSstatsTMT |
| Version: 1.6.6 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSstatsTMT_1.6.6.tar.gz |
| StartedAt: 2020-10-17 03:29:57 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:32:54 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 176.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MSstatsTMT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSstatsTMT_1.6.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘1.6.6’
* 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 39.642 0.180 39.287
groupComparisonTMT 19.048 0.092 18.468
proteinSummarization 6.520 0.047 5.894
* 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: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MSstatsTMT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(MSstatsTMT)
>
> 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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|================================================= | 70%
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|======================================================== | 80%
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|=============================================================== | 90%
|
|======================================================================| 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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|======================================================== | 80%
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|=============================================================== | 90%
|
|======================================================================| 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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|=============================================================== | 90%
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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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|=============================================================== | 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%
|
|======================================================================| 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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|======================================================== | 80%
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|=============================================================== | 90%
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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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|=============================================================== | 90%
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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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|======= | 10%
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|================================================= | 70%
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|======================================================== | 80%
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|=============================================================== | 90%
|
|======================================================================| 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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|======= | 10%
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|======================================================== | 80%
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|=============================================================== | 90%
|
|======================================================================| 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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|======= | 10%
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|================================================= | 70%
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|======================================================== | 80%
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|=============================================================== | 90%
|
|======================================================================| 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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|======= | 10%
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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 3-34
# 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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|======= | 10%
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|========================================== | 60%
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|================================================= | 70%
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|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 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
|
| | 0%
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|======= | 10%
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|============== | 20%
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|===================== | 30%
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|============================ | 40%
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|========================================== | 60%
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|================================================= | 70%
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|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 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
|
| | 0%
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|======= | 10%
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|===================== | 30%
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|======================================================================| 100%
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
26.911 0.333 26.024
MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings
| name | user | system | elapsed | |
| MaxQtoMSstatsTMTFormat | 0.516 | 0.032 | 0.548 | |
| OpenMStoMSstatsTMTFormat | 0.516 | 0.012 | 0.527 | |
| PDtoMSstatsTMTFormat | 1.503 | 0.008 | 1.511 | |
| SpectroMinetoMSstatsTMTFormat | 0.527 | 0.012 | 0.540 | |
| annotation.mine | 0.003 | 0.000 | 0.003 | |
| annotation.mq | 0.003 | 0.000 | 0.003 | |
| annotation.pd | 0.004 | 0.000 | 0.003 | |
| dataProcessPlotsTMT | 39.642 | 0.180 | 39.287 | |
| evidence | 0.012 | 0.004 | 0.016 | |
| groupComparisonTMT | 19.048 | 0.092 | 18.468 | |
| input.pd | 0.003 | 0.004 | 0.007 | |
| proteinGroups | 0.071 | 0.012 | 0.083 | |
| proteinSummarization | 6.520 | 0.047 | 5.894 | |
| quant.pd.msstats | 0.006 | 0.000 | 0.005 | |
| raw.mine | 0.013 | 0.000 | 0.013 | |
| raw.om | 0.007 | 0.000 | 0.007 | |
| raw.pd | 0.011 | 0.000 | 0.011 | |
| test.pairwise | 0.004 | 0.000 | 0.004 | |