Bo Wen
| Snapshot Date: 2019-10-01 17:01:25 -0400 (Tue, 01 Oct 2019) |
| URL: https://git.bioconductor.org/packages/proteoQC |
| Branch: RELEASE_3_9 |
| Last Commit: 20a400d |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-02 12:53:14 -0400 (Wed, 02 Oct 2019).
| Package 1269/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| proteoQC 1.20.0 Bo Wen
| 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: proteoQC |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proteoQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proteoQC_1.20.0.tar.gz |
| StartedAt: 2019-10-02 05:41:09 -0400 (Wed, 02 Oct 2019) |
| EndedAt: 2019-10-02 05:45:11 -0400 (Wed, 02 Oct 2019) |
| EllapsedTime: 241.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: proteoQC.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:proteoQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings proteoQC_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/proteoQC.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 ‘proteoQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘proteoQC’ version ‘1.20.0’ * 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 ‘proteoQC’ 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 ... NOTE Found the following apparent S3 methods exported but not registered: print.msQCres See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calcMSQCMetrics :: warning in readMSData(x, msLevel = 1): partial argument match of 'msLevel' to 'msLevel.' calcMSQCMetrics : : warning in readMSData(x, msLevel = 2): partial argument match of 'msLevel' to 'msLevel.' addSummaryChart: no visible binding for global variable ‘peplength’ addSummaryChart: no visible binding for global variable ‘..count..’ addSummaryChart: no visible binding for global variable ‘delta’ chargeStat: no visible global function definition for ‘readMgfData’ chargeStat: no visible global function definition for ‘precursorCharge’ ggplot.RT: no visible binding for global variable ‘x’ ggplot.RT: no visible binding for global variable ‘y’ ggplot.RT: no visible binding for global variable ‘techRep’ ggplot.RT: no visible binding for global variable ‘bioRep’ labelRatio: no visible global function definition for ‘readMgfData’ labelRatio: no visible binding for global variable ‘iTRAQ4’ labelRatio: no visible binding for global variable ‘iTRAQ8’ labelRatio: no visible binding for global variable ‘TMT6’ labelRatio: no visible binding for global variable ‘TMT10’ labelRatio: no visible global function definition for ‘exprs’ labelRatio: no visible global function definition for ‘quantify’ labelRatio: no visible binding for global variable ‘Tag’ labelRatio: no visible binding for global variable ‘Intensity’ labelRatio: no visible binding for global variable ‘ratio’ labelRatio: no visible binding for global variable ‘label’ msQC.barplot: no visible binding for global variable ‘x’ msQC.barplot: no visible binding for global variable ‘y’ msQC.barplot: no visible binding for global variable ‘label’ plotBioRepVenn : : no visible global function definition for ‘grid.draw’ plotMS1Count: no visible binding for global variable ‘bioRep’ plotMS1Count: no visible binding for global variable ‘techRep’ plotMS1Count: no visible binding for global variable ‘fraction’ plotMS1Count: no visible binding for global variable ‘MS1QC’ plotMS1CountErrorBar: no visible binding for global variable ‘bioRep’ plotMS1CountErrorBar: no visible binding for global variable ‘techRep’ plotMS1CountErrorBar: no visible binding for global variable ‘fraction’ plotMS1CountErrorBar: no visible binding for global variable ‘MS1QC’ plotMS1CountErrorBar: no visible binding for global variable ‘val’ plotMS1CountErrorBar: no visible binding for global variable ‘se’ plotMS1Error: no visible binding for '<<-' assignment to ‘curenv’ plotMS1Error: no visible binding for global variable ‘bioRep’ plotMS1Error: no visible binding for global variable ‘techRep’ plotMS1Error: no visible binding for global variable ‘fraction’ plotMS1Error: no visible binding for global variable ‘peptide_summary’ plotMS1Error: no visible binding for global variable ‘curenv’ plotMS1Error : : no visible binding for global variable ‘curenv’ plotMS1IonCount: no visible binding for global variable ‘bioRep’ plotMS1IonCount: no visible binding for global variable ‘techRep’ plotMS1IonCount: no visible binding for global variable ‘fraction’ plotMS1IonCount: no visible binding for global variable ‘MS1QC’ plotMS1PeaksCount: no visible binding for global variable ‘bioRep’ plotMS1PeaksCount: no visible binding for global variable ‘techRep’ plotMS1PeaksCount: no visible binding for global variable ‘fraction’ plotMS1PeaksCount: no visible binding for global variable ‘MS1QC’ plotMS1TIC: no visible binding for global variable ‘bioRep’ plotMS1TIC: no visible binding for global variable ‘techRep’ plotMS1TIC: no visible binding for global variable ‘fraction’ plotMS1TIC: no visible binding for global variable ‘MS1QC’ plotMS1boxplot: no visible binding for global variable ‘bioRep’ plotMS1boxplot: no visible binding for global variable ‘techRep’ plotMS1boxplot: no visible binding for global variable ‘fraction’ plotMS1boxplot: no visible binding for global variable ‘MS1QC’ plotMS2Error: no visible binding for global variable ‘bioRep’ plotMS2Error: no visible binding for global variable ‘techRep’ plotMS2Error: no visible binding for global variable ‘fraction’ plotMS2Error: no visible binding for global variable ‘V1’ plotMS2Error: no visible binding for global variable ‘V2’ plotMS2Error: no visible binding for global variable ‘V3’ plotMS2Error: no visible binding for global variable ‘V4’ plotMS2Error: no visible binding for global variable ‘V5’ plotMS2Error_obsolete: no visible binding for global variable ‘bioRep’ plotMS2Error_obsolete: no visible binding for global variable ‘techRep’ plotMS2Error_obsolete: no visible binding for global variable ‘fraction’ plotMS2Error_obsolete: no visible binding for global variable ‘peptide_summary’ plotMS2PeakFreq: no visible binding for global variable ‘bioRep’ plotMS2PeakFreq: no visible binding for global variable ‘techRep’ plotMS2PeakFreq: no visible binding for global variable ‘fraction’ plotMS2PeakFreq: no visible binding for global variable ‘MS2QC’ plotMS2boxplot: no visible binding for global variable ‘bioRep’ plotMS2boxplot: no visible binding for global variable ‘techRep’ plotMS2boxplot: no visible binding for global variable ‘fraction’ plotMS2boxplot: no visible binding for global variable ‘MS2QC’ plotSampleIDResultErrorBar: no visible binding for global variable ‘fraction’ plotSampleIDResultErrorBar: no visible binding for global variable ‘val’ plotSampleIDResultErrorBar: no visible binding for global variable ‘se’ plotSampleVenn: no visible global function definition for ‘grid.draw’ plotTechRepVenn : : no visible global function definition for ‘grid.draw’ qcHist: no visible binding for global variable ‘error’ qcHist: no visible binding for global variable ‘techRep’ qcHist: no visible binding for global variable ‘bioRep’ qcHist2: no visible binding for global variable ‘error’ qcHist2: no visible binding for global variable ‘fractile’ Undefined global functions or variables: ..count.. Intensity MS1QC MS2QC TMT10 TMT6 Tag V1 V2 V3 V4 V5 bioRep curenv delta error exprs fractile fraction grid.draw iTRAQ4 iTRAQ8 label peplength peptide_summary precursorCharge quantify ratio readMgfData se techRep val x y * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed labelRatio 96.476 4.230 34.551 chargeStat 8.824 0.125 8.960 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/proteoQC.Rcheck/00check.log’ for details.
proteoQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL proteoQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘proteoQC’ ... ** using staged installation ** R ** 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 (proteoQC)
proteoQC.Rcheck/tests/runTests.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.
> BiocGenerics:::testPackage("proteoQC")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
This is MSnbase version 2.10.1
Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
RUNIT TEST PROTOCOL -- Wed Oct 2 05:45:03 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
proteoQC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.817 0.850 8.624
proteoQC.Rcheck/proteoQC-Ex.timings
| name | user | system | elapsed | |
| chargeStat | 8.824 | 0.125 | 8.960 | |
| labelRatio | 96.476 | 4.230 | 34.551 | |
| loadmsQCres | 0.095 | 0.158 | 0.286 | |
| msQCpipe | 0.001 | 0.001 | 0.002 | |
| print.msQCres | 0.098 | 0.119 | 0.218 | |
| proteinGroup | 0.939 | 0.509 | 0.655 | |
| reportHTML | 0.094 | 0.100 | 0.195 | |
| showEnzyme | 0.006 | 0.001 | 0.008 | |
| showMods | 0.003 | 0.001 | 0.005 | |