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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1222/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mia 1.13.0  (landing page)
Tuomas Borman
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/mia
git_branch: devel
git_last_commit: f257732
git_last_commit_date: 2024-04-30 11:32:24 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for mia on palomino4

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: 1.13.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mia.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mia_1.13.0.tar.gz
StartedAt: 2024-06-10 05:19:15 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:43:39 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 1464.5 seconds
RetCode: 0
Status:   OK  
CheckDir: mia.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mia.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings mia_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'mia/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mia' version '1.13.0'
* 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 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                  84.12   0.03   85.50
runCCA                        48.64   0.50   49.14
hierarchy-tree                22.15   1.39   23.55
estimateDiversity             11.88   1.44   13.30
makeTreeSEFromDADA2            8.34   1.90   10.95
agglomerate-methods            9.66   0.55   10.22
splitByRanks                   8.36   0.54    8.90
mergeSEs                       6.47   0.53    7.02
getExperimentCrossAssociation  6.19   0.29    6.50
getPrevalence                  5.63   0.47    6.11
splitOn                        5.62   0.47    6.10
calculateJSD                   4.74   0.43    5.17
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck/00check.log'
for details.


Installation output

mia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL mia
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

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 7.46 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 
 579.56   99.20  681.90 

Example timings

mia.Rcheck/mia-Ex.timings

nameusersystemelapsed
addCluster1.450.281.74
addDivergence1.500.421.92
agglomerate-methods 9.66 0.5510.22
calculateDMN84.12 0.0385.50
calculateJSD4.740.435.17
calculateOverlap0.160.040.19
calculateUnifrac0.460.070.54
estimateDiversity11.88 1.4413.30
estimateDominance0.260.060.33
estimateEvenness0.080.020.09
estimateRichness0.500.050.55
getExperimentCrossAssociation6.190.296.50
getPrevalence5.630.476.11
hierarchy-tree22.15 1.3923.55
importHUMAnN0.360.010.39
importMetaPhlAn3.510.193.72
importMothur0.260.000.30
importQIIME21.180.451.78
isContaminant0.350.020.37
makePhyloseqFromTreeSE2.190.582.80
makeTreeSEFromBiom0.740.080.85
makeTreeSEFromDADA2 8.34 1.9010.95
makeTreeSEFromPhyloseq1.700.171.90
meltAssay0.860.411.27
merge-methods1.500.532.11
mergeSEs6.470.537.02
mia-datasets0.530.330.85
perSampleDominantTaxa2.030.412.44
relabundance0.380.260.64
runCCA48.64 0.5049.14
runDPCoA0.480.080.57
runNMDS0.360.020.38
splitByRanks8.360.548.90
splitOn5.620.476.10
subsampleCounts1.600.251.83
subsetSamples0.950.351.30
summaries3.330.533.86
taxonomy-methods1.200.341.54
transformAssay0.270.020.28