Multiple platform build/check report for BioC 3.19 - CHECK results for mia on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4466
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*

CHECK results for mia on merida1

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: 1.12.0

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

StartedAt: 2024-06-24 07:28:40 -0400 (Mon, 24 Jun 2024)

EndedAt: 2024-06-24 08:08:41 -0400 (Mon, 24 Jun 2024)

EllapsedTime: 2401.0 seconds

RetCode: None

Status: TIMEOUT

CheckDir: mia.Rcheck

Warnings: NA

Command output

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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
###
##############################################################################
##############################################################################


* 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 12.7.4
* 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
calculateDMN                  102.162  0.492 119.030
runCCA                         94.190  1.007 112.149
hierarchy-tree                 52.189  1.405  60.818
agglomerate-methods            24.629  0.539  28.617
splitByRanks                   21.174  0.273  25.243
estimateDiversity              19.456  1.221  23.411
mergeSEs                       17.574  0.296  20.243
getExperimentCrossAssociation  17.002  0.141  20.406
getPrevalence                  13.187  0.130  15.900
makeTreeSEFromDADA2            12.488  0.533  14.355
splitOn                        10.872  0.089  12.904
summaries                       9.071  0.090  10.398
importMetaPhlAn                 8.985  0.060   9.811
calculateJSD                    7.659  0.666   9.380
perSampleDominantTaxa           6.019  0.077   6.602
addDivergence                   4.648  0.190   6.619
makePhyloseqFromTreeSE          4.578  0.144   5.268
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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/4.4-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)

Tests output

mia.Rcheck/tests/testthat.Rout


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 11.7 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.

Example timings

mia.Rcheck/mia-Ex.timings

name	user	system	elapsed
addCluster	2.311	0.045	2.987
addDivergence	4.648	0.190	6.619
agglomerate-methods	24.629	0.539	28.617
calculateDMN	102.162	0.492	119.030
calculateJSD	7.659	0.666	9.380
calculateOverlap	0.439	0.012	0.479
calculateUnifrac	0.950	0.024	1.051
estimateDiversity	19.456	1.221	23.411
estimateDominance	0.773	0.025	0.884
estimateEvenness	0.207	0.018	0.241
estimateRichness	0.918	0.073	1.084
getExperimentCrossAssociation	17.002	0.141	20.406
getPrevalence	13.187	0.130	15.900
hierarchy-tree	52.189	1.405	60.818
importHUMAnN	0.785	0.008	0.852
importMetaPhlAn	8.985	0.060	9.811
importMothur	0.652	0.010	0.729
importQIIME2	2.499	0.273	3.047
isContaminant	1.006	0.017	1.130
makePhyloseqFromTreeSE	4.578	0.144	5.268
makeTreeSEFromBiom	1.643	0.021	1.863
makeTreeSEFromDADA2	12.488	0.533	14.355
makeTreeSEFromPhyloseq	3.288	0.046	3.764
meltAssay	1.686	0.041	1.947
merge-methods	3.628	0.114	4.278
mergeSEs	17.574	0.296	20.243
mia-datasets	1.142	0.018	1.344
perSampleDominantTaxa	6.019	0.077	6.602
relabundance	0.877	0.015	0.948
runCCA	94.190	1.007	112.149
runDPCoA	1.008	0.024	1.273
runNMDS	0.844	0.019	1.035
splitByRanks	21.174	0.273	25.243
splitOn	10.872	0.089	12.904
subsampleCounts	3.192	0.043	3.765
subsetSamples	2.211	0.026	2.613
summaries	9.071	0.090	10.398
taxonomy-methods	2.850	0.035	3.481
transformAssay	0.561	0.012	0.687