##############################################################################
##############################################################################
###
### 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/mia.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘topicdoc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘picante’
Unknown package ‘https’ in Rd xrefs
Non-topic package-anchored link(s) in Rd file 'calculateDMN.Rd':
  ‘[DirichletMultinomial:fitted]{accessors for DMN objects}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addCluster.Rd: BlusterParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
addNMF                42.355 11.243  39.323
calculateDMN          47.929  0.251  48.452
agglomerate-methods   20.706  0.962  21.834
hierarchy-tree        17.175  1.372  18.607
transformAssay        10.175  0.526  10.729
splitOn                9.964  0.480  10.482
getPrevalence          7.513  0.248   7.786
getDissimilarity       6.149  1.252   7.384
addAlpha               6.936  0.338   7.312
addLDA                 6.082  0.173   6.286
convertFromDADA2       5.730  0.331   6.101
getCrossAssociation    5.967  0.057   6.052
utilization_functions  5.364  0.217   5.623
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Differences:
  1/1 mismatches
  x[1]: "BCNMKCKTTVWYCKKMHTTMYTKKKYKTMMMKNKHDYKYMKDYKKNHNNNYMMKHHNDNNKTKMMMDNBHNBK
  x[1]: KCTYMMCHNBNDDDNKSSHBNNRWDMYKKBNNDNYTDRRKDVHNKNDRVGRNDRSBRRAWTBYNHRKKKWRSSR
  x[1]: KKRAAWKSSKWRRWDWTNDBRVRRAMHHCMRDKKSSRARGSSVSYYHNYBRRVHNDNNHYKRMVVYKVRDNNNS
  x[1]: RAARSBDKGGKK"
  y[1]: "SCRAGCGTTRTCCGGAWTTAYTGGGYKTAAAGSGMGCGYAGGYGGHBDNKYAAGTCWGWWGTGAAAKYYYGSG
  y[1]: GCTCAACCSYRRRMBKSCWKTKGAAACTGBVHKRCTWGAKTKYVKDWGAGGWRRGYGGAATKCSWVGTGTAGCG
  y[1]: GTGAAATGCKTAGAKATBWSGARGAACWCCRRTKGCGAAGGCRRCTYWCTRGWCKGWVAMTGACGCTGAKGCKC
  y[1]: GAAAGYGTGGGK"
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1342 ]
  Error:
  ! Test failures.
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/mia.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mia
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘mia’ ...
** this is package ‘mia’ version ‘1.19.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c assay.cpp -o assay.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c faith_R.cpp -o faith_R.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c propmap.cpp -o propmap.o
In file included from propmap.cpp:12:
./propmap.h:31:18: warning: private field 'defaultsize' is not used [-Wunused-private-field]
        uint32_t defaultsize;
                 ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c transformCounts.cpp -o transformCounts.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tree.cpp -o tree.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mia.so RcppExports.o assay.o faith_R.o propmap.o transformCounts.o tree.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/00LOCK-mia/00new/mia/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mia)

R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 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: MultiAssayExperiment
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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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

This is mia version 1.19.0
- Online documentation and vignettes: https://microbiome.github.io/mia/
- Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
> 
> test_check("mia")
================================================================================

Time difference of 6.25 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.




Saving _problems/test-5prevalence-511.R
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 1 | WARN 2 | SKIP 0 | PASS 1342 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-5prevalence.R:506:5'): agglomerateByPrevalence ───────────────
Expected `as.character(referenceSeq(actual)[["Alistipes"]])` to equal `paste0(...)`.
Differences:
1/1 mismatches
x[1]: "BCNMKCKTTVWYCKKMHTTMYTKKKYKTMMMKNKHDYKYMKDYKKNHNNNYMMKHHNDNNKTKMMMDNBHNBK
x[1]: KCTYMMCHNBNDDDNKSSHBNNRWDMYKKBNNDNYTDRRKDVHNKNDRVGRNDRSBRRAWTBYNHRKKKWRSSR
x[1]: KKRAAWKSSKWRRWDWTNDBRVRRAMHHCMRDKKSSRARGSSVSYYHNYBRRVHNDNNHYKRMVVYKVRDNNNS
x[1]: RAARSBDKGGKK"
y[1]: "SCRAGCGTTRTCCGGAWTTAYTGGGYKTAAAGSGMGCGYAGGYGGHBDNKYAAGTCWGWWGTGAAAKYYYGSG
y[1]: GCTCAACCSYRRRMBKSCWKTKGAAACTGBVHKRCTWGAKTKYVKDWGAGGWRRGYGGAATKCSWVGTGTAGCG
y[1]: GTGAAATGCKTAGAKATBWSGARGAACWCCRRTKGCGAAGGCRRCTYWCTRGWCKGWVAMTGACGCTGAKGCKC
y[1]: GAAAGYGTGGGK"

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 1342 ]
Error:
! Test failures.
Execution halted