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This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).

CHECK results for mia on tokay2

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
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raw results

Package 1124/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mia 1.0.8  (landing page)
Felix G.M. Ernst
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/mia
git_branch: RELEASE_3_13
git_last_commit: 95eeac0
git_last_commit_date: 2021-07-30 16:13:43 -0400 (Fri, 30 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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    OK    OK  UNNEEDED, same version is already published

Summary

Package: mia
Version: 1.0.8
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mia_1.0.8.tar.gz
StartedAt: 2021-10-15 01:52:18 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:10:40 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 1102.1 seconds
RetCode: 0
Status:   OK  
CheckDir: mia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mia.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings mia_1.0.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/mia.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mia/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mia' version '1.0.8'
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
splitByRanks                          15.18   0.45   15.64
taxonomy-methods                      14.61   0.48   15.09
calculateJSD                           9.37   1.40   10.78
estimateDiversity                      9.71   0.41   10.12
getPrevalence                          9.75   0.12    9.87
agglomerate-methods                    9.12   0.65    9.78
makeTreeSummarizedExperimentFromDADA2  8.97   0.19   10.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
splitByRanks                          15.40   0.27   15.67
taxonomy-methods                      15.28   0.33   15.61
getPrevalence                         11.16   0.11   11.26
estimateDiversity                     10.29   0.13   10.42
agglomerate-methods                    8.75   0.22    8.96
calculateJSD                           6.80   0.66    7.45
makeTreeSummarizedExperimentFromDADA2  7.28   0.17    7.45
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/mia.Rcheck/00check.log'
for details.

Installation output

mia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/mia_1.0.8.tar.gz && rm -rf mia.buildbin-libdir && mkdir mia.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mia.buildbin-libdir mia_1.0.8.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL mia_1.0.8.zip && rm mia_1.0.8.tar.gz mia_1.0.8.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1599k  100 1599k    0     0  2827k      0 --:--:-- --:--:-- --:--:-- 2831k

install for i386

* installing *source* package 'mia' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mia'
    finding HTML links ... done
    agglomerate-methods                     html  
    calculateDMN                            html  
    calculateDistance                       html  
    calculateJSD                            html  
    calculateUniFrac                        html  
    estimateDivergence                      html  
    finding level-2 HTML links ... done

    estimateDiversity                       html  
    estimateDominance                       html  
    estimateEvenness                        html  
    estimateRichness                        html  
    getAbundance                            html  
    getPrevalence                           html  
    isContaminant                           html  
    loadFromMothur                          html  
    loadFromQIIME2                          html  
    makePhyloseqFromTreeSummarizedExperiment
                                            html  
    makeSummarizedExperimentFromBiom        html  
    makeTreeSummarizedExperimentFromDADA2   html  
    makeTreeSummarizedExperimentFromphyloseq
                                            html  
    meltAssay                               html  
    merge-methods                           html  
    mia-datasets                            html  
    mia-package                             html  
    perSampleDominantTaxa                   html  
    relabundance                            html  
    runCCA                                  html  
    runDPCoA                                html  
    runNMDS                                 html  
    splitByRanks                            html  
    subsetSamples                           html  
    summaries                               html  
    taxonomy-methods                        html  
    transformCounts                         html  
** 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

install for x64

* installing *source* package 'mia' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mia' as mia_1.0.8.zip
* DONE (mia)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'mia' successfully unpacked and MD5 sums checked

Tests output

mia.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

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

> 
> test_check("mia")
================================================================================

Time difference of 12.38 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 605 ]
> 
> proc.time()
   user  system elapsed 
 276.57    8.20  287.61

mia.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

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

> 
> test_check("mia")
================================================================================

Time difference of 9.26 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 605 ]
> 
> proc.time()
   user  system elapsed 
 274.00    5.39  280.96

Example timings

mia.Rcheck/examples_i386/mia-Ex.timings

nameusersystemelapsed
agglomerate-methods9.120.659.78
calculateDMN2.500.024.41
calculateDistance0.020.000.02
calculateJSD 9.37 1.4010.78
calculateUniFrac1.170.051.22
estimateDivergence2.240.222.45
estimateDiversity 9.71 0.4110.12
estimateDominance0.630.010.64
estimateEvenness0.140.020.16
estimateRichness0.70.00.7
getAbundance0.640.140.79
getPrevalence9.750.129.87
isContaminant0.490.020.50
loadFromMothur0.080.000.19
loadFromQIIME21.640.154.48
makePhyloseqFromTreeSummarizedExperiment1.980.132.11
makeSummarizedExperimentFromBiom0.080.000.08
makeTreeSummarizedExperimentFromDADA2 8.97 0.1910.03
makeTreeSummarizedExperimentFromphyloseq2.370.342.84
meltAssay0.860.130.99
merge-methods1.800.212.01
perSampleDominantTaxa2.330.112.44
relabundance0.480.110.60
runCCA2.280.192.46
runDPCoA0.530.110.65
runNMDS0.430.020.45
splitByRanks15.18 0.4515.64
subsetSamples1.520.111.62
summaries2.870.143.02
taxonomy-methods14.61 0.4815.09
transformCounts0.790.020.80

mia.Rcheck/examples_x64/mia-Ex.timings

nameusersystemelapsed
agglomerate-methods8.750.228.96
calculateDMN1.800.021.93
calculateDistance0.050.000.05
calculateJSD6.800.667.45
calculateUniFrac0.390.000.39
estimateDivergence1.790.101.89
estimateDiversity10.29 0.1310.42
estimateDominance0.640.020.66
estimateEvenness0.160.000.15
estimateRichness0.690.010.71
getAbundance0.540.090.64
getPrevalence11.16 0.1111.26
isContaminant0.520.000.52
loadFromMothur0.060.000.06
loadFromQIIME22.250.222.84
makePhyloseqFromTreeSummarizedExperiment1.510.111.63
makeSummarizedExperimentFromBiom0.080.000.08
makeTreeSummarizedExperimentFromDADA27.280.177.45
makeTreeSummarizedExperimentFromphyloseq2.160.052.20
meltAssay0.860.130.99
merge-methods2.190.172.36
perSampleDominantTaxa2.860.122.98
relabundance0.680.130.83
runCCA2.470.192.69
runDPCoA0.740.000.73
runNMDS0.470.010.49
splitByRanks15.40 0.2715.67
subsetSamples1.250.091.34
summaries2.530.082.61
taxonomy-methods15.28 0.3315.61
transformCounts0.880.000.88