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CHECK report for MetCirc on malbec1

This page was generated on 2019-04-16 11:52:10 -0400 (Tue, 16 Apr 2019).

Package 929/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetCirc 1.12.1
Thomas Naake
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MetCirc
Branch: RELEASE_3_8
Last Commit: 942d673
Last Changed Date: 2019-01-04 13:38:47 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MetCirc
Version: 1.12.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MetCirc_1.12.1.tar.gz
StartedAt: 2019-04-16 01:18:02 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:19:27 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 84.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MetCirc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MetCirc_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MetCirc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetCirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetCirc’ version ‘1.12.1’
* 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 ‘MetCirc’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘circlize:::get.sector.data’
  See the note in ?`:::` about the use of this operator.
* 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
allocatePrecursor2mz 5.604  0.148    5.76
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/MetCirc.Rcheck/00check.log’
for details.



Installation output

MetCirc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MetCirc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MetCirc’ ...
** R
** data
** 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
* DONE (MetCirc)

Tests output

MetCirc.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(amap)
> library(circlize)
========================================
circlize version 0.4.6
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization 
  in R. Bioinformatics 2014.
========================================

> library(scales)
> library(shiny)
> 
> data("sd01_outputXCMS", package = "MetCirc")
> data("sd02_deconvoluted", package = "MetCirc")
> data("binnedMSP", package = "MetCirc")
> data("similarityMat", package = "MetCirc")
> 
> BiocGenerics:::testPackage("MetCirc")
[1] "13"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "15"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "16"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "20"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "21"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "23"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "24"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "25"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "26"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "27"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "28"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "29"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "30"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "31"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "32"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "44"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "45"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "46"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "47"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "48"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "49"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "50"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "51"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "52"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "53"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "54"                                                                                                
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "54"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "55"                                                                                                
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "55"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "56"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "59"                                                                                                
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "59"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "60"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "61"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "62"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "63"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "64"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "65"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "66"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "67"                                                                                                
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "67"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "68"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "71"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "72"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "73"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "74"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "75"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "76"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "77"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "78"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "79"                                                                                                
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "79"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "80"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "81"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "82"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "83"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "84"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "85"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "86"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "89"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "90"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "91"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "92"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "93"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "94"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "95"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "96"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "97"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "98"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "99"                                                                                                   
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "100"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "101"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "102"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "103"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "103"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "104"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "105"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "106"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "107"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "108"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "109"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "110"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "112"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "113"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "115"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "116"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "118"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "119"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "120"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "121"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "122"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "123"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "124"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "125"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "126"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "127"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "128"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "129"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "130"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "131"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "132"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "133"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "135"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "136"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "137"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "138"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "139"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "140"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "141"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "142"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "143"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "144"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "145"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "146"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "147"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "150"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "151"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "152"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "153"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "154"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "155"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "156"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "157"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "158"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "159"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "160"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "161"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "162"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "163"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "164"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "165"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "166"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "167"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "168"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "169"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "170"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "171"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "172"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "173"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "174"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "175"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "176"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "177"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "177"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "178"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "178"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "179"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "179"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "181"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "182"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "183"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "184"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "185"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "186"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "187"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "188"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "190"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "191"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "192"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "193"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "194"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "195"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "196"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "197"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "198"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "199"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "200"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "201"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "202"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "203"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "204"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "204"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "208"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "209"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "212"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "213"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "214"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "215"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "215"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "216"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "216"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "217"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "217"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "218"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "219"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "222"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "223"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "225"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "226"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "227"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "228"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "229"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "230"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "231"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "232"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "233"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "234"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "235"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "237"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "238"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "240"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "241"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "242"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "243"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "244"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "245"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "246"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "248"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "249"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "250"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "251"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "252"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "254"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "254"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "255"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "256"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "257"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "258"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "259"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "260"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "261"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "262"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "263"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "264"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "265"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "266"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "267"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "268"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "269"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "269"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "270"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "271"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "272"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "272"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "274"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "275"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "276"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "277"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "278"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "278"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "279"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "280"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "281"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "282"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "283"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "284"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "285"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "286"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "287"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "288"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "289"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "290"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "291"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "292"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "292"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "293"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "294"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "295"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "296"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "297"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "298"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "299"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "300"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "301"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "303"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "304"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "305"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "306"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "308"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "309"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "311"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "313"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "314"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "315"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "316"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "316"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "317"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "318"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "319"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "320"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "321"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "322"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "323"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "324"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "325"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "326"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "327"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "328"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "328"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "329"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "330"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "331"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "332"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "333"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "334"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "335"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "336"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "337"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "338"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "339"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "340"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "341"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "342"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "343"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "345"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "346"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "347"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "347"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "348"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "349"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "350"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "351"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "352"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "353"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "354"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "355"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "356"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "357"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "358"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "359"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
[1] "360"                                                                                               
[2] "Deviation of m/z is greater than tolerance value. \n                     I won't truncate the kNN."
[1] "360"                                                                                                  
[2] "Deviation of rt is greater than tolerance value. \n                    I won't use rt as a criterion."
An object of class MSP with 360 entries.

RUNIT TEST PROTOCOL -- Tue Apr 16 01:19:23 2019 
*********************************************** 
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MetCirc RUnit Tests - 39 test functions, 0 errors, 0 failures
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 
Warning message:
In warning_wrap("'gap.degree' can only be modified before `circos.initialize`, or maybe you forgot to call `circos.clear` in your last plot.") :
  'gap.degree' can only be modified before `circos.initialize`, or maybe
you forgot to call `circos.clear` in your last plot.
> 
> proc.time()
   user  system elapsed 
 21.144   0.096  21.284 

Example timings

MetCirc.Rcheck/MetCirc-Ex.timings

nameusersystemelapsed
NDP0.0200.0080.029
adduct-set0.2640.0200.285
adduct0.2720.0000.275
allocatePrecursor2mz5.6040.1485.760
binning1.9280.2682.199
cart2Polar000
circosLegend0.6680.0040.672
classes-set0.5360.0000.535
classes0.5240.0000.525
combine0.9320.0000.933
convert2MSP0.4400.0040.445
convertMSP2MSP0.0160.0000.016
createLink0Matrix0.1040.0000.103
createLinkMatrix0.7280.0120.741
createOrderedSimMat1.2760.3441.620
createSimilarityMatrix0.0880.0080.097
cutLinkMatrix1.0480.0041.054
cutUniquePrecursor0.0000.0000.001
extract-methods0.4120.0000.410
getBegEndIndMSP0.4280.0000.431
getLinkMatrixIndices0.0000.0000.001
getPrecursorMZ0.2800.0000.282
getRT0.3240.0000.326
highlight1.6880.0081.700
information-set0.3000.0000.299
information0.4120.0040.415
length-method0.4280.0000.427
minFragCart2Polar1.2840.0001.290
msp2FunctionalLossesMSP0.5160.0000.514
names-set0.3960.0000.398
names0.4120.0000.411
peaks0.5200.0320.552
plotCircos2.3800.0042.387
printInformationSelect1.1200.0001.119
shinyCircos0.4720.0000.474
show-method0.4160.0000.415
thresholdLinkMatrix1.1080.0081.116
truncateName0.0000.0000.001