Multiple platform build/check report for BioC 3.10 - CHECK report for MetCirc on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MetCirc_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MetCirc.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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 ‘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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/MetCirc.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MetCirc
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘MetCirc’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘MSnbase’ for request: ‘Spectra’ when loading ‘MetCirc’
No methods found in package ‘MSnbase’ for request: ‘Spectrum2’ when loading ‘MetCirc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘MSnbase’ for request: ‘Spectra’ when loading ‘MetCirc’
No methods found in package ‘MSnbase’ for request: ‘Spectrum2’ when loading ‘MetCirc’
** testing if installed package can be loaded from final location
No methods found in package ‘MSnbase’ for request: ‘Spectra’ when loading ‘MetCirc’
No methods found in package ‘MSnbase’ for request: ‘Spectrum2’ when loading ‘MetCirc’
** testing if installed package keeps a record of temporary installation path
* DONE (MetCirc)

Tests output


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> library(amap)
> library(circlize)
========================================
circlize version 0.4.8
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")
> 
> BiocGenerics:::testPackage("MetCirc")

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


Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.12.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    trimws

No methods found in package 'MSnbase' for request: 'Spectra' when loading 'MetCirc'
No methods found in package 'MSnbase' for request: 'Spectrum2' when loading 'MetCirc'
Note: 1 point is out of plotting region in sector 'SPL_241', track '1'.
Note: 1 point is out of plotting region in sector 'LIM_34', track '1'.
Note: 1 point is out of plotting region in sector 'ANT_16', track '1'.
Note: 1 point is out of plotting region in sector 'STY_124', track '1'.


RUNIT TEST PROTOCOL -- Wed Apr 15 03:59:47 2020 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MetCirc RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
103.888   0.284 105.632

Example timings

name	user	system	elapsed
cart2Polar	0	0	0
circosLegend	1.412	0.028	1.476
compare_Spectra	0.180	0.000	0.181
convertMsp2Spectra	0.308	0.008	0.318
createLink0df	2.072	0.028	2.110
createLinkDf	4.772	0.036	4.839
cutLinkDf	2.652	0.016	2.670
getLinkDfIndices	0	0	0
highlight	1.200	0.004	1.204
minFragCart2Polar	0.568	0.012	0.579
neutralloss	0.016	0.000	0.017
normalizeddotproduct	0.016	0.000	0.015
orderSimilarityMatrix	0.524	0.000	0.521
plotCircos	1.248	0.000	1.251
plotSpectra	0.388	0.008	0.399
printInformationSelect	0.800	0.000	0.802
recordPlotFill_degreeFeatures	0.148	0.004	0.163
recordPlotHighlight	0.152	0.000	0.154
replayPlotAdd	1.420	0.004	1.431
replayPlotOrder	0.184	0.004	0.190
select	0	0	0
spectraCond	0.020	0.000	0.019
thresholdLinkDf	2.340	0.024	2.379
typeMatch_link0	0.692	0.008	0.702

CHECK report for MetCirc on malbec1

Summary

Command output

Installation output

Tests output

Example timings