Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:05:45 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 nebbiolo1


To the developers/maintainers of the mia package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1167/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mia 1.4.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/mia
git_branch: RELEASE_3_15
git_last_commit: 18fd690
git_last_commit_date: 2022-04-26 12:14:03 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mia
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings mia_1.4.0.tar.gz
StartedAt: 2022-05-17 20:21:04 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 20:31:38 -0400 (Tue, 17 May 2022)
EllapsedTime: 634.7 seconds
RetCode: 0
Status:   OK  
CheckDir: mia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings mia_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/mia.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.4.0’
* 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 R 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 ... NOTE
.get_experiment_cross_association: no visible global function
  definition for ‘unfactor’
Undefined global functions or variables:
  unfactor
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
taxonomy-methods                      18.462  0.448  18.910
getExperimentCrossAssociation         11.520  1.140  13.503
agglomerate-methods                   12.129  0.260  12.399
estimateDiversity                      9.364  0.123   9.489
makeTreeSummarizedExperimentFromDADA2  7.616  0.288   7.904
getPrevalence                          6.697  0.432   7.128
splitByRanks                           6.348  0.072   6.420
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/mia.Rcheck/00check.log’
for details.



Installation output

mia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL mia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
** 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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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 8.78 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
initial  value 0.000000 
final  value 0.000000 
converged
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 708 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 708 ]
> 
> proc.time()
   user  system elapsed 
275.363   6.979 284.014 

Example timings

mia.Rcheck/mia-Ex.timings

nameusersystemelapsed
agglomerate-methods12.129 0.26012.399
calculateDMN1.1230.0041.127
calculateDistance0.1340.0000.135
calculateJSD3.8870.1764.063
calculateOverlap0.1560.0030.160
calculateUnifrac0.2510.0170.268
estimateDivergence1.4400.0041.444
estimateDiversity9.3640.1239.489
estimateDominance0.30.00.3
estimateEvenness0.0800.0010.079
estimateRichness0.3660.0030.370
getAbundance0.4480.2090.656
getExperimentCrossAssociation11.520 1.14013.503
getPrevalence6.6970.4327.128
isContaminant0.4520.0360.488
loadFromMetaphlan1.2530.0321.285
loadFromMothur0.2610.0000.262
loadFromQIIME21.1640.0721.238
makePhyloseqFromTreeSummarizedExperiment1.7500.0961.846
makeSummarizedExperimentFromBiom0.3000.0080.308
makeTreeSummarizedExperimentFromDADA27.6160.2887.904
makeTreeSummarizedExperimentFromPhyloseq1.4890.0791.570
meltAssay0.7790.0880.867
merge-methods1.4230.0561.480
perSampleDominantTaxa3.3720.1883.560
relabundance0.3980.0000.399
runCCA1.5060.0921.598
runDPCoA0.3940.0160.410
runNMDS0.3210.0320.353
splitByRanks6.3480.0726.420
subsampleCounts1.3850.0321.417
subsetSamples0.9010.0040.905
summaries2.8640.0882.952
taxonomy-methods18.462 0.44818.910
transformCounts0.5170.0080.524