Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:59:01 -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: /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_1.6.6.tar.gz |
StartedAt: 2020-10-17 03:21:02 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 03:24:54 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 232.2 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_1.6.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MSstatsTMT.Rcheck’ * using R version 4.0.3 (2020-10-10) * 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 ‘1.6.6’ * 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 51.148 0.649 52.167 groupComparisonTMT 19.370 0.319 19.829 proteinSummarization 8.714 0.292 9.022 * 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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 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") 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 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% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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 | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 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% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 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% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100% ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 30.253 0.987 31.308
MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings
name | user | system | elapsed | |
MaxQtoMSstatsTMTFormat | 0.628 | 0.087 | 0.716 | |
OpenMStoMSstatsTMTFormat | 0.686 | 0.017 | 0.707 | |
PDtoMSstatsTMTFormat | 2.014 | 0.048 | 2.065 | |
SpectroMinetoMSstatsTMTFormat | 0.504 | 0.042 | 0.545 | |
annotation.mine | 0.004 | 0.001 | 0.004 | |
annotation.mq | 0.004 | 0.001 | 0.004 | |
annotation.pd | 0.002 | 0.001 | 0.003 | |
dataProcessPlotsTMT | 51.148 | 0.649 | 52.167 | |
evidence | 0.022 | 0.014 | 0.037 | |
groupComparisonTMT | 19.370 | 0.319 | 19.829 | |
input.pd | 0.011 | 0.002 | 0.012 | |
proteinGroups | 0.127 | 0.056 | 0.184 | |
proteinSummarization | 8.714 | 0.292 | 9.022 | |
quant.pd.msstats | 0.006 | 0.001 | 0.007 | |
raw.mine | 0.016 | 0.003 | 0.019 | |
raw.om | 0.008 | 0.001 | 0.010 | |
raw.pd | 0.013 | 0.004 | 0.016 | |
test.pairwise | 0.005 | 0.002 | 0.006 | |