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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miaViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miaViz_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/miaViz.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miaViz/DESCRIPTION’ ... OK
* this is package ‘miaViz’ version ‘1.10.0’
* package encoding: UTF-8
* 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 ‘miaViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.rda_plotter: no visible binding for global variable ‘color’
Undefined global functions or variables:
  color
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
plotTree             51.461  1.139  52.690
plotDMN              18.784  0.034  18.883
plotAbundanceDensity 15.024  1.211  18.875
plotAbundance         9.554  0.483  10.129
plotPrevalence        8.822  0.116   8.970
plotCCA               6.849  0.156   7.109
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/miaViz.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miaViz
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘miaViz’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (miaViz)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(miaViz)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: TreeSummarizedExperiment
Loading required package: SingleCellExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: mia
Loading required package: MultiAssayExperiment
Loading required package: ggplot2
Loading required package: ggraph
> 
> test_check("miaViz")
matrixStats (1.2.0  -> 1.3.0 ) [CRAN]
igraph      (2.0.2  -> 2.0.3 ) [CRAN]
tidyselect  (1.2.0  -> 1.2.1 ) [CRAN]
munsell     (0.5.0  -> 0.5.1 ) [CRAN]
ragg        (1.2.7  -> 1.3.0 ) [CRAN]
uwot        (0.1.16 -> 0.2.1 ) [CRAN]
RSQLite     (2.3.5  -> 2.3.6 ) [CRAN]
digest      (0.6.34 -> 0.6.35) [CRAN]
ape         (5.7-1  -> 5.8   ) [CRAN]
trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/matrixStats_1.3.0.tgz'
Content type 'application/x-gzip' length 630178 bytes (615 KB)
==================================================
downloaded 615 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/igraph_2.0.3.tgz'
Content type 'application/x-gzip' length 9659207 bytes (9.2 MB)
==================================================
downloaded 9.2 MB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/tidyselect_1.2.1.tgz'
Content type 'application/x-gzip' length 224103 bytes (218 KB)
==================================================
downloaded 218 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/munsell_0.5.1.tgz'
Content type 'application/x-gzip' length 244085 bytes (238 KB)
==================================================
downloaded 238 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/ragg_1.3.0.tgz'
Content type 'application/x-gzip' length 10892373 bytes (10.4 MB)
==================================================
downloaded 10.4 MB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/uwot_0.1.16.tgz'
Content type 'application/x-gzip' length 3941361 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/RSQLite_2.3.6.tgz'
Content type 'application/x-gzip' length 4371485 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/digest_0.6.35.tgz'
Content type 'application/x-gzip' length 352093 bytes (343 KB)
==================================================
downloaded 343 KB

trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.3/ape_5.8.tgz'
Content type 'application/x-gzip' length 3487904 bytes (3.3 MB)
==================================================
downloaded 3.3 MB


The downloaded binary packages are in
	/tmp/RtmpAoz8M6/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/private/tmp/RtmpAoz8M6/remotese1733eba00cb/microbiome-miaTime-9fe9771/DESCRIPTION’ ... OK
* preparing ‘miaTime’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘miaTime_0.1.21.tar.gz’

* installing *source* package ‘miaTime’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (miaTime)
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 215 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 215 ]
> 
> proc.time()
   user  system elapsed 
156.269  19.993 189.268