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This page was generated on 2025-08-23 12:06 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1265/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mia 1.17.5  (landing page)
Tuomas Borman
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 Aug 2025)
git_url: https://git.bioconductor.org/packages/mia
git_branch: devel
git_last_commit: 95ee8b1
git_last_commit_date: 2025-07-07 17:09:54 -0400 (Mon, 07 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for mia on kjohnson3

To the developers/maintainers of the mia package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mia.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mia
Version: 1.17.5
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_1.17.5.tar.gz
StartedAt: 2025-08-22 20:15:34 -0400 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 20:29:52 -0400 (Fri, 22 Aug 2025)
EllapsedTime: 857.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: mia.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.17.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mia.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.17.5’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.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 ... NOTE
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
calculateDMN        28.676  0.022  28.812
addNMF              16.416  3.799  15.692
agglomerate-methods  7.953  0.431   8.628
hierarchy-tree       6.318  0.656   7.295
* 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:
  x[1]: KCTYMMCHNBNDDDNKSSHBNNRWDMYKKBNNDNYTDRRKDVHNKNDRVGRNDRSBRRAWTBYNHRKKKWRSSR
  x[1]: KKRAAWKSSKWRRWDWTNDBRVRRAMHHCMRDKKSSRARGSSVSYYHNYBRRVHNDNNHYKRMVVYKVRDNNNS
  x[1]: RAARSBDKGGKK"
  y[1]: "SCRAGCGTTRTCCGGAWTTAYTGGGYKTAAAGSGMGCGYAGGYGGHBDNKYAAGTCWGWWGTGAAAKYYYGSG
  y[1]: GCTCAACCSYRRRMBKSCWKTKGAAACTGBVHKRCTWGAKTKYVKDWGAGGWRRGYGGAATKCSWVGTGTAGCG
  y[1]: GTGAAATGCKTAGAKATBWSGARGAACWCCRRTKGCGAAGGCRRCTYWCTRGWCKGWVAMTGACGCTGAKGCKC
  y[1]: GAAAGYGTGGGK"
  ── Error ('test-mediate.R:69:3'): getMediation ─────────────────────────────────
  Error in `mediate(fit_m, fit_dv, treat = "Treatment", mediator = "Mediator", 
      treat.value = "Scandinavia", control.value = "CentralEurope", 
      boot = TRUE, sims = 1)`: could not find function "mediate"
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 1285 ]
  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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/mia.Rcheck/00check.log’
for details.


Installation output

mia.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘mia’ ...
** this is package ‘mia’ version ‘1.17.5’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c assay.cpp -o assay.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c faith_R.cpp -o faith_R.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tree.cpp -o tree.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o mia.so RcppExports.o assay.o faith_R.o propmap.o tree.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)

Tests output

mia.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 1.17.5
- 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 3.71 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 2 | WARN 3 | SKIP 0 | PASS 1285 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-5prevalence.R:506:5'): agglomerateByPrevalence ───────────────
as.character(referenceSeq(actual)[["Alistipes"]]) not equal to paste0(...).
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"
── Error ('test-mediate.R:69:3'): getMediation ─────────────────────────────────
Error in `mediate(fit_m, fit_dv, treat = "Treatment", mediator = "Mediator", 
    treat.value = "Scandinavia", control.value = "CentralEurope", 
    boot = TRUE, sims = 1)`: could not find function "mediate"

[ FAIL 2 | WARN 3 | SKIP 0 | PASS 1285 ]
Error: Test failures
Execution halted

Example timings

mia.Rcheck/mia-Ex.timings

nameusersystemelapsed
addAlpha4.0850.1154.223
addCluster0.2110.0140.227
addDivergence0.5360.0420.579
addLDA3.5940.0373.634
addMDS1.1690.0531.226
addNMF16.416 3.79915.692
agglomerate-methods7.9530.4318.628
agglomerateByPrevalence0.9300.0360.996
calculateDMN28.676 0.02228.812
convertFromDADA22.1950.1182.330
convertFromPhyloseq1.1330.0741.212
getAbundant0.7580.0170.786
getCrossAssociation2.2370.0252.281
getDissimilarity3.5260.6214.134
getDominant1.1110.0491.177
getMediation0.0000.0000.001
getPERMANOVA0.5140.0420.560
getPrevalence3.3760.1453.603
hierarchy-tree6.3180.6567.295
importBIOM0.1690.0040.173
importHUMAnN0.0570.0010.059
importMetaPhlAn0.7140.0090.729
importMothur0.0640.0020.068
importQIIME20.2100.0430.260
importTaxpasta000
isContaminant0.1150.0030.119
meltSE0.3850.0370.424
mergeSEs2.0080.0622.088
mia-datasets0.1740.0030.177
rarefyAssay0.4180.0130.432
runCCA1.5880.0521.659
runDPCoA0.1130.0060.119
runNMDS0.0700.0040.085
splitOn4.4970.2684.804
summary1.6360.0301.666
taxonomy-methods0.4820.0100.497
transformAssay3.5810.1603.752
utilization_functions2.3030.0582.377