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"	4757
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4480
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4511
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4469
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: 2024-07-01 07:36:59 -0400 (Mon, 01 Jul 2024)

EndedAt: 2024-07-01 08:17:00 -0400 (Mon, 01 Jul 2024)

EllapsedTime: 2400.7 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                  101.867  0.591 124.012
runCCA                         94.804  0.877 112.220
hierarchy-tree                 53.399  1.497  66.928
agglomerate-methods            24.713  0.571  30.688
splitByRanks                   21.061  0.244  25.501
estimateDiversity              19.280  1.229  23.620
mergeSEs                       17.552  0.285  20.528
getExperimentCrossAssociation  16.912  0.153  19.340
getPrevalence                  13.349  0.141  15.385
makeTreeSEFromDADA2            12.475  0.533  15.149
splitOn                        10.950  0.091  12.842
summaries                       9.069  0.098  10.912
importMetaPhlAn                 9.013  0.081  10.355
calculateJSD                    7.501  0.663   9.366
perSampleDominantTaxa           6.047  0.067   7.240
addDivergence                   4.733  0.203   6.141
makePhyloseqFromTreeSE          4.523  0.148   5.325
* 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 12.1 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	2.398	0.043	3.039
addDivergence	4.733	0.203	6.141
agglomerate-methods	24.713	0.571	30.688
calculateDMN	101.867	0.591	124.012
calculateJSD	7.501	0.663	9.366
calculateOverlap	0.436	0.012	0.498
calculateUnifrac	0.938	0.030	1.105
estimateDiversity	19.280	1.229	23.620
estimateDominance	0.794	0.031	1.012
estimateEvenness	0.217	0.020	0.278
estimateRichness	0.972	0.075	1.187
getExperimentCrossAssociation	16.912	0.153	19.340
getPrevalence	13.349	0.141	15.385
hierarchy-tree	53.399	1.497	66.928
importHUMAnN	0.785	0.011	0.874
importMetaPhlAn	9.013	0.081	10.355
importMothur	0.681	0.011	0.799
importQIIME2	2.531	0.272	3.358
isContaminant	0.993	0.017	1.206
makePhyloseqFromTreeSE	4.523	0.148	5.325
makeTreeSEFromBiom	1.682	0.023	2.108
makeTreeSEFromDADA2	12.475	0.533	15.149
makeTreeSEFromPhyloseq	3.264	0.044	3.769
meltAssay	1.691	0.050	1.986
merge-methods	3.625	0.112	4.256
mergeSEs	17.552	0.285	20.528
mia-datasets	1.157	0.015	1.341
perSampleDominantTaxa	6.047	0.067	7.240
relabundance	0.920	0.015	1.098
runCCA	94.804	0.877	112.220
runDPCoA	0.998	0.020	1.181
runNMDS	0.853	0.016	1.024
splitByRanks	21.061	0.244	25.501
splitOn	10.950	0.091	12.842
subsampleCounts	3.248	0.044	3.805
subsetSamples	2.230	0.025	2.611
summaries	9.069	0.098	10.912
taxonomy-methods	2.832	0.033	3.378
transformAssay	0.550	0.014	0.656