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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).

CHECK results for MetCirc on nebbiolo1

To the developers/maintainers of the MetCirc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetCirc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1096/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetCirc 1.22.0  (landing page)
Thomas Naake
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MetCirc
git_branch: RELEASE_3_13
git_last_commit: ff94e6d
git_last_commit_date: 2021-05-19 12:21:11 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MetCirc
Version: 1.22.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MetCirc_1.22.0.tar.gz
StartedAt: 2021-10-14 10:31:30 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:34:54 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 203.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MetCirc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MetCirc_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MetCirc.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.22.0’
* 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 ‘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 objects imported by ':::' calls:
  ‘MSnbase:::bin_Spectra’ ‘circlize:::get.sector.data’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘recordPlotFill_degreeFeatures’ ‘recordPlotHighlight’ ‘replayPlotAdd’
  ‘replayPlotOrder’ ‘select’ ‘spectraCond’ ‘typeMatch_link0’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotSpectra: no visible binding for global variable ‘mz’
plotSpectra: no visible binding for global variable ‘int’
Undefined global functions or variables:
  int mz
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/MetCirc.Rcheck/00check.log’
for details.



Installation output

MetCirc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MetCirc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MetCirc’ ...
** using staged installation
** 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 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 (MetCirc)

Tests output

MetCirc.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("MetCirc")
Loading required package: amap
Loading required package: circlize
========================================
circlize version 0.4.13
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://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.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================

Loading required package: scales
Loading required package: shiny
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

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.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.18.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:base':

    trimws

> 
> test_check("MetCirc")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 72.472   1.035  73.465 

Example timings

MetCirc.Rcheck/MetCirc-Ex.timings

nameusersystemelapsed
cart2Polar000
circosLegend1.1890.0521.241
compare_Spectra0.1390.0000.139
convertMsp2Spectra0.1740.0280.201
createLink0df1.2930.0521.345
createLinkDf2.8680.1242.992
cutLinkDf1.4270.0561.482
getLinkDfIndices000
highlight1.4170.0081.425
minFragCart2Polar0.6630.0040.667
neutralloss0.0140.0000.015
normalizeddotproduct0.0130.0000.014
orderSimilarityMatrix0.5090.0040.512
plotCircos0.7270.0070.734
plotSpectra0.2150.0000.214
printInformationSelect0.5840.0040.588
recordPlotFill_degreeFeatures0.0960.0000.096
recordPlotHighlight0.0940.0000.095
replayPlotAdd1.3580.0121.370
replayPlotOrder0.1250.0040.129
select000
shinyCircos0.5030.0000.502
spectraCond0.0090.0040.012
thresholdLinkDf1.4470.1241.572
typeMatch_link00.5480.0200.568