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This page was generated on 2022-04-13 12:06:53 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 microbiomeMarker on tokay2


To the developers/maintainers of the microbiomeMarker package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiomeMarker.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 1144/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.0.2  (landing page)
Yang Cao
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: RELEASE_3_14
git_last_commit: ea467f1
git_last_commit_date: 2022-03-07 10:09:50 -0400 (Mon, 07 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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: microbiomeMarker
Version: 1.0.2
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiomeMarker.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings microbiomeMarker_1.0.2.tar.gz
StartedAt: 2022-04-12 22:50:39 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:02:28 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 709.3 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeMarker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiomeMarker.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings microbiomeMarker_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/microbiomeMarker.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiomeMarker/DESCRIPTION' ... OK
* this is package 'microbiomeMarker' version '1.0.2'
* 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 'microbiomeMarker' 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 ... 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 ... 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 R/sysdata.rda ... 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
run_aldex      10.66   1.10   11.86
plot_cladogram  9.50   0.62   10.13
run_deseq2      9.30   0.02    9.31
run_ancombc     7.92   0.01    7.94
plot_heatmap    7.37   0.22    7.59
plot_sl_roc     6.17   0.14    6.32
run_lefse       5.22   0.16    5.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
run_aldex      11.17   1.17   12.37
run_deseq2      9.49   0.00    9.49
plot_cladogram  9.34   0.13    9.47
run_ancombc     8.54   0.00    8.55
plot_sl_roc     6.40   0.03    6.44
plot_heatmap    6.22   0.10    6.32
run_lefse       6.05   0.10    6.14
* 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: OK

Installation output

microbiomeMarker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/microbiomeMarker_1.0.2.tar.gz && rm -rf microbiomeMarker.buildbin-libdir && mkdir microbiomeMarker.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiomeMarker.buildbin-libdir microbiomeMarker_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL microbiomeMarker_1.0.2.zip && rm microbiomeMarker_1.0.2.tar.gz microbiomeMarker_1.0.2.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
  2 1589k    2 37587    0     0   237k      0  0:00:06 --:--:--  0:00:06  238k
 64 1589k   64 1024k    0     0   886k      0  0:00:01  0:00:01 --:--:--  886k
100 1589k  100 1589k    0     0  1063k      0  0:00:01  0:00:01 --:--:-- 1063k

install for i386

* installing *source* package 'microbiomeMarker' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'microbiomeMarker'
    finding HTML links ... done
    abundances-methods                      html  
    finding level-2 HTML links ... done

    aggregate_taxa                          html  
    assign-marker_table                     html  
    assign-otu_table                        html  
    data-caporaso                           html  
    data-cid_ying                           html  
    data-ecam                               html  
    data-enterotypes_arumugam               html  
    data-kostic_crc                         html  
    data-oxygen                             html  
    data-pediatric_ibd                      html  
    data-spontaneous_colitis                html  
    effect_size-plot                        html  
    extract-methods                         html  
    extract_posthoc_res                     html  
    get_treedata_phyloseq                   html  
    import_dada2                            html  
    import_picrust2                         html  
    import_qiime2                           html  
    marker_table-class                      html  
    marker_table-methods                    html  
    microbiomeMarker-class                  html  
    microbiomeMarker-package                html  
    microbiomeMarker                        html  
    nmarker-methods                         html  
    normalize-methods                       html  
    phyloseq2DESeq2                         html  
    phyloseq2edgeR                          html  
    phyloseq2metagenomeSeq                  html  
    plot_abundance                          html  
    plot_cladogram                          html  
    plot_heatmap                            html  
    plot_postHocTest                        html  
    plot_sl_roc                             html  
    postHocTest-class                       html  
    postHocTest                             html  
    reexports                               html  
    run_aldex                               html  
    run_ancom                               html  
    run_ancombc                             html  
    run_deseq2                              html  
    run_edger                               html  
    run_lefse                               html  
    run_limma_voom                          html  
    run_marker                              html  
    run_metagenomeseq                       html  
    run_posthoc_test                        html  
    run_simple_stat                         html  
    run_sl                                  html  
    run_test_multiple_groups                html  
    run_test_two_groups                     html  
    subset_marker                           html  
    summarize_taxa                          html  
    transform_abundances                    html  
*** 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

install for x64

* installing *source* package 'microbiomeMarker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiomeMarker' as microbiomeMarker_1.0.2.zip
* DONE (microbiomeMarker)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'microbiomeMarker' successfully unpacked and MD5 sums checked

Tests output

microbiomeMarker.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(microbiomeMarker)
> 
> test_check("microbiomeMarker")
operating in serial mode
computing center with all features
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
operating in serial mode
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
Default value being used.
Default value being used.
Default value being used.
Default value being used.
converting counts to integer mode
Loading required package: ggplot2
Loading required package: lattice
[ FAIL 0 | WARN 26 | SKIP 8 | PASS 194 ]

== Skipped tests ===============================================================
* On CRAN (7)
* empty test (1)

[ FAIL 0 | WARN 26 | SKIP 8 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
  77.73    4.20   82.03

microbiomeMarker.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(microbiomeMarker)
> 
> test_check("microbiomeMarker")
operating in serial mode
computing center with all features
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
operating in serial mode
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
New names:
* `` -> `...1`
* `` -> `...2`
* `` -> `...3`
* `` -> `...4`
* `` -> `...5`
* `` -> `...6`
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
Also defined by 'tidytree'
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
`set.seed(2020)` was used to initialize repeatable random subsampling.
Please record this for your records so others can reproduce.
Try `set.seed(2020); .Random.seed` for the full vector
...
46OTUs were removed because they are no longer 
present in any sample after random subsampling

...
Default value being used.
Default value being used.
Default value being used.
Default value being used.
converting counts to integer mode
Loading required package: ggplot2
Loading required package: lattice
[ FAIL 0 | WARN 26 | SKIP 8 | PASS 194 ]

== Skipped tests ===============================================================
* On CRAN (7)
* empty test (1)

[ FAIL 0 | WARN 26 | SKIP 8 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
  73.76    2.29   76.06

Example timings

microbiomeMarker.Rcheck/examples_i386/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.120.000.13
aggregate_taxa0.380.050.42
assign-marker_table2.880.643.52
effect_size-plot3.110.003.11
extract_posthoc_res0.110.020.12
import_dada20.080.010.09
import_picrust20.050.000.07
import_qiime20.350.060.77
marker_table-methods3.580.023.59
microbiomeMarker0.010.000.02
nmarker-methods000
normalize-methods0.140.000.14
phyloseq2DESeq20.740.030.76
phyloseq2edgeR0.170.020.19
phyloseq2metagenomeSeq0.190.000.19
plot_abundance4.200.034.23
plot_cladogram 9.50 0.6210.13
plot_heatmap7.370.227.59
plot_postHocTest1.070.031.09
plot_sl_roc6.170.146.32
postHocTest0.080.000.08
run_aldex10.66 1.1011.86
run_ancom000
run_ancombc7.920.017.94
run_deseq29.300.029.31
run_edger2.900.002.91
run_lefse5.220.165.40
run_limma_voom3.800.003.89
run_metagenomeseq4.110.074.19
run_posthoc_test0.590.030.63
run_simple_stat2.770.022.78
run_sl2.860.002.86
run_test_multiple_groups2.890.022.90
run_test_two_groups2.810.002.82
subset_marker2.50.02.5
summarize_taxa0.310.010.32
transform_abundances0.210.030.27

microbiomeMarker.Rcheck/examples_x64/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.100.000.09
aggregate_taxa1.280.031.32
assign-marker_table3.190.053.24
effect_size-plot3.090.033.12
extract_posthoc_res0.150.000.14
import_dada20.070.000.08
import_picrust20.030.000.03
import_qiime20.300.020.31
marker_table-methods2.860.012.88
microbiomeMarker0.020.000.01
nmarker-methods000
normalize-methods0.110.020.13
phyloseq2DESeq20.790.010.81
phyloseq2edgeR0.140.020.16
phyloseq2metagenomeSeq0.160.030.19
plot_abundance4.530.004.53
plot_cladogram9.340.139.47
plot_heatmap6.220.106.32
plot_postHocTest1.070.021.08
plot_sl_roc6.400.036.44
postHocTest0.100.000.09
run_aldex11.17 1.1712.37
run_ancom000
run_ancombc8.540.008.55
run_deseq29.490.009.49
run_edger3.050.003.05
run_lefse6.050.106.14
run_limma_voom3.30.03.3
run_metagenomeseq4.760.004.77
run_posthoc_test0.690.000.68
run_simple_stat3.280.003.29
run_sl2.910.012.92
run_test_multiple_groups3.790.003.79
run_test_two_groups3.880.023.89
subset_marker3.060.003.06
summarize_taxa0.590.000.60
transform_abundances0.180.010.18