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This page was generated on 2021-12-03 13:04:53 -0500 (Fri, 03 Dec 2021).

CHECK results for mia on nebbiolo2

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? here 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 1137/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mia 1.2.3  (landing page)
Felix G.M. Ernst
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/mia
git_branch: RELEASE_3_14
git_last_commit: 0c44333
git_last_commit_date: 2021-11-27 04:30:49 -0500 (Sat, 27 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: mia
Version: 1.2.3
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mia_1.2.3.tar.gz
StartedAt: 2021-12-02 07:58:21 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 08:08:57 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 636.2 seconds
RetCode: 0
Status:   OK  
CheckDir: mia.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:mia.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings mia_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/mia.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.2.3’
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.test_experiment_of_mae: no visible global function definition for
  ‘experiments’
Undefined global functions or variables:
  experiments
* 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
getExperimentCrossCorrelation         18.950  0.544  20.262
taxonomy-methods                      14.832  0.112  14.943
getPrevalence                         12.975  0.208  13.183
agglomerate-methods                   12.017  0.636  12.654
estimateDiversity                     12.058  0.372  12.430
splitByRanks                          10.963  0.028  10.991
makeTreeSummarizedExperimentFromDADA2  9.344  0.072   9.418
calculateJSD                           5.417  0.112   5.548
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/mia.Rcheck/00check.log’
for details.



Installation output

mia.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL mia
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 9.08 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 0 | SKIP 0 | PASS 645 ]
> 
> proc.time()
   user  system elapsed 
273.860   9.029 284.481 

Example timings

mia.Rcheck/mia-Ex.timings

nameusersystemelapsed
agglomerate-methods12.017 0.63612.654
calculateDMN0.8900.0020.891
calculateDistance0.0310.0000.031
calculateJSD5.4170.1125.548
calculateUniFrac0.3890.0000.389
estimateDivergence1.7850.0001.787
estimateDiversity12.058 0.37212.430
estimateDominance0.5040.0000.505
estimateEvenness0.1180.0000.119
estimateRichness0.7220.0040.726
getAbundance0.4860.0400.525
getExperimentCrossCorrelation18.950 0.54420.262
getPrevalence12.975 0.20813.183
isContaminant0.5520.0040.556
loadFromMothur0.0660.0000.067
loadFromQIIME21.2190.0121.239
makePhyloseqFromTreeSummarizedExperiment2.6910.3002.995
makeSummarizedExperimentFromBiom0.0700.0000.069
makeTreeSummarizedExperimentFromDADA29.3440.0729.418
makeTreeSummarizedExperimentFromPhyloseq2.1740.0202.195
meltAssay0.9030.0680.971
merge-methods2.0030.0002.003
perSampleDominantTaxa2.6630.0042.669
relabundance0.4880.0000.489
runCCA1.8870.0041.890
runDPCoA0.5720.0000.573
runNMDS0.3620.0000.362
splitByRanks10.963 0.02810.991
subsetSamples1.2280.0001.240
summaries2.6460.0042.650
taxonomy-methods14.832 0.11214.943
transformCounts0.7800.0040.784