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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.12.0’
* 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 ‘mia’ 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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) agglomerate-methods.Rd:73-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:78-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agglomerate-methods.Rd:84-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:94-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:149-151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:153-162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:164-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:167-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:178-183: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:185-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDiversity.Rd:194: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:99-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:103-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:114-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:128-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:139-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:149-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateDominance.Rd:160-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateEvenness.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateEvenness.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateEvenness.Rd:73-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateEvenness.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateEvenness.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateEvenness.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateRichness.Rd:87-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateRichness.Rd:106-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateRichness.Rd:119-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimateRichness.Rd:128-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExperimentCrossAssociation.Rd:66-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getExperimentCrossAssociation.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hierarchy-tree.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hierarchy-tree.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) importHUMAnN.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importHUMAnN.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importHUMAnN.Rd:23-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:32-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:35-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importMetaPhlAn.Rd:40-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importQIIME2.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) importQIIME2.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isContaminant.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) isContaminant.Rd:86-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeTreeSEFromBiom.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) meltAssay.Rd:67-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) taxonomy-methods.Rd:101-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) taxonomy-methods.Rd:116-117: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy-methods.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomy-methods.Rd:119-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) transformAssay.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:157-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:160-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:163-164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:166-167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:169-170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:172-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:178-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:184-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:187-188: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:190-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:193-194: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:196-197: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:199-200: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:202-203: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:205-207: Lost braces in \itemize; meant \describe ?
checkRd: (-1) transformAssay.Rd:209-210: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘https’ in Rd xrefs
* 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 ... NOTE
  Note: found 101 marked UTF-8 strings
* 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
runCCA                        59.094  0.708  60.296
calculateDMN                  58.275  0.517  59.315
hierarchy-tree                26.204  1.647  28.140
estimateDiversity             12.781  1.691  14.637
agglomerate-methods           12.899  0.374  13.408
splitByRanks                   9.871  0.212  10.153
mergeSEs                       8.777  0.194   9.051
getExperimentCrossAssociation  8.277  0.134   8.503
makeTreeSEFromDADA2            7.361  0.440   7.878
getPrevalence                  6.438  0.139   6.649
calculateJSD                   5.450  0.818   6.328
splitOn                        5.334  0.076   5.446
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/mia.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mia
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘mia’ ...
** 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 (mia)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(mia)
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, 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: SingleCellExperiment
Loading required package: TreeSummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: MultiAssayExperiment
> 
> test_check("mia")
================================================================================

Time difference of 7.99 secs

Initializing error rates to maximum possible estimate.
selfConsist step 1 .
   selfConsist step 2
   selfConsist step 3
   selfConsist step 4
Convergence after  4  rounds.
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
   selfConsist step 2
   selfConsist step 3
   selfConsist step 4
Convergence after  4  rounds.
initial  value 0.383462 
iter   5 value 0.161655
iter  10 value 0.113278
final  value 0.003270 
converged
initial  value 0.000000 
final  value 0.000000 
converged
initial  value 0.000000 
final  value 0.000000 
converged
[ FAIL 0 | WARN 66 | SKIP 2 | PASS 957 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• require("miaTime", quietly = TRUE) is not TRUE (2): 'test-2mergeSEs.R:382:5',
  'test-3agglomerate.R:88:5'

[ FAIL 0 | WARN 66 | SKIP 2 | PASS 957 ]
> 
> proc.time()
   user  system elapsed 
616.630 115.593 739.986