Multiple platform build/check report for BioC 3.11 - CHECK report for MetCirc on tokay2

Package: MetCirc

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetCirc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MetCirc_1.18.0.tar.gz

StartedAt: 2020-10-17 05:52:17 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 05:59:58 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 461.0 seconds

RetCode: 0

Status: OK

CheckDir: MetCirc.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MetCirc.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MetCirc_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MetCirc.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetCirc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetCirc' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
createLinkDf 5.94   0.01    5.95
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MetCirc.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MetCirc_1.18.0.tar.gz && rm -rf MetCirc.buildbin-libdir && mkdir MetCirc.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MetCirc.buildbin-libdir MetCirc_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MetCirc_1.18.0.zip && rm MetCirc_1.18.0.tar.gz MetCirc_1.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1574k  100 1574k    0     0  19.6M      0 --:--:-- --:--:-- --:--:-- 21.3M

install for i386

* 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
  converting help for package 'MetCirc'
    finding HTML links ... done
    cart2Polar                              html  
    circosLegend                            html  
    compare_Spectra                         html  
    compartmentTissue                       html  
    convertExampleDF                        html  
    convertMsp2Spectra                      html  
    createLink0df                           html  
    createLinkDf                            html  
    cutLinkDf                               html  
    getLinkDfIndices                        html  
    highlight                               html  
    minFragCart2Polar                       html  
    msp2spectra                             html  
    neutralloss                             html  
    normalizeddotproduct                    html  
    orderSimilarityMatrix                   html  
    plotCircos                              html  
    plotSpectra                             html  
    printInformationSelect                  html  
    recordPlotFill_degreeFeatures           html  
    recordPlotHighlight                     html  
    replayPlotAdd                           html  
    replayPlotOrder                         html  
    sd01_outputXCMS                         html  
    sd02_deconvoluted                       html  
    select                                  html  
    shinyCircos                             html  
    similarityMat                           html  
    spectraCond                             html  
    spectra_tissue                          html  
    thresholdLinkDf                         html  
    tissue                                  html  
    typeMatch_link0                         html  
** 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

install for x64

* installing *source* package 'MetCirc' ...
** testing if installed package can be loaded
No methods found in package 'MSnbase' for request: 'Spectra' when loading 'MetCirc'
No methods found in package 'MSnbase' for request: 'Spectrum2' when loading 'MetCirc'
* MD5 sums
packaged installation of 'MetCirc' as MetCirc_1.18.0.zip
* DONE (MetCirc)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MetCirc' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 0.4.10
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))
========================================

> 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 2.14.2 
  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 -- Sat Oct 17 05:57:51 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 
  92.84    0.64   93.48


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 0.4.10
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))
========================================

> 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 2.14.2 
  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 -- Sat Oct 17 05:59:50 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 
 117.62    0.39  118.12

name	user	system	elapsed
cart2Polar	0	0	0
circosLegend	1.34	0.10	1.44
compare_Spectra	0.26	0.00	0.26
convertMsp2Spectra	0.25	0.01	0.27
createLink0df	2.72	0.07	2.78
createLinkDf	5.94	0.01	5.95
cutLinkDf	2.84	0.00	2.84
getLinkDfIndices	0	0	0
highlight	1.53	0.08	1.61
minFragCart2Polar	1.17	0.00	1.17
neutralloss	0.05	0.00	0.05
normalizeddotproduct	0.03	0.00	0.03
orderSimilarityMatrix	1.23	0.02	1.25
plotCircos	1.22	0.01	1.23
plotSpectra	0.35	0.00	0.35
printInformationSelect	0.76	0.00	0.76
recordPlotFill_degreeFeatures	0.1	0.0	0.1
recordPlotHighlight	0.09	0.00	0.10
replayPlotAdd	1.67	0.03	1.70
replayPlotOrder	0.22	0.00	0.21
select	0	0	0
spectraCond	0.03	0.00	0.04
thresholdLinkDf	1.95	0.01	1.96
typeMatch_link0	0.63	0.04	0.66

name	user	system	elapsed
cart2Polar	0	0	0
circosLegend	1.19	0.02	1.20
compare_Spectra	0.19	0.00	0.19
convertMsp2Spectra	0.29	0.03	0.33
createLink0df	3.19	0.01	3.20
createLinkDf	3.87	0.08	3.95
cutLinkDf	3.31	0.02	3.33
getLinkDfIndices	0	0	0
highlight	1.68	0.01	1.69
minFragCart2Polar	0.78	0.00	0.79
neutralloss	0.02	0.02	0.03
normalizeddotproduct	0.01	0.00	0.01
orderSimilarityMatrix	0.63	0.00	0.63
plotCircos	0.95	0.00	0.95
plotSpectra	0.24	0.00	0.24
printInformationSelect	1	0	1
recordPlotFill_degreeFeatures	0.11	0.00	0.10
recordPlotHighlight	0.10	0.00	0.11
replayPlotAdd	1.04	0.00	1.04
replayPlotOrder	0.15	0.00	0.15
select	0	0	0
spectraCond	0.02	0.00	0.02
thresholdLinkDf	2.73	0.05	2.78
typeMatch_link0	0.86	0.01	0.87

CHECK report for MetCirc on tokay2

Summary

Command output

Installation output

Tests output

Example timings