Multiple platform build/check report for BioC 3.14 - CHECK results for phyloseq on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: phyloseq

Version: 1.38.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phyloseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings phyloseq_1.38.0.tar.gz

StartedAt: 2022-04-13 00:31:04 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:38:39 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 454.9 seconds

RetCode: 0

Status: OK

CheckDir: phyloseq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phyloseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings phyloseq_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/phyloseq.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 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.38.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'phyloseq' 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 ... NOTE
DPCoA: no visible global function definition for 'as.dist'
chunkReOrder: no visible global function definition for 'tail'
chunkReOrder: no visible global function definition for 'head'
export_env_file: no visible global function definition for
  'write.table'
export_mothur_dist: no visible global function definition for 'as.dist'
export_mothur_dist: no visible global function definition for
  'write.table'
fastUniFrac: no visible global function definition for 'combn'
fastUniFrac: no visible global function definition for 'as.dist'
import_RDP_otu: no visible global function definition for 'read.table'
import_env_file: no visible global function definition for 'read.table'
import_mothur_constaxonomy: no visible global function definition for
  'read.table'
import_mothur_dist: no visible global function definition for 'as.dist'
import_mothur_groups: no visible global function definition for
  'read.table'
import_mothur_shared: no visible global function definition for
  'read.table'
import_qiime_otu_tax: no visible global function definition for ':='
import_qiime_otu_tax: no visible binding for global variable 'Consensus
  Lineage'
import_qiime_otu_tax: no visible binding for global variable '#OTU ID'
import_qiime_sample_data: no visible global function definition for
  'read.table'
import_uparse: no visible global function definition for ':='
import_uparse: no visible binding for global variable 'count'
import_uparse: no visible binding for global variable 'queryString'
import_uparse: no visible binding for global variable 'queryID'
import_uparse: no visible binding for global variable 'Classification'
import_uparse: no visible global function definition for
  'dcast.data.table'
import_uparse: no visible binding for global variable 'OTULabel'
import_usearch_uc: no visible global function definition for ':='
import_usearch_uc: no visible binding for global variable 'read'
microbio_me_qiime: no visible global function definition for
  'download.file'
microbio_me_qiime: no visible global function definition for 'unzip'
microbio_me_qiime: no visible global function definition for 'untar'
nodeplotboot : <anonymous>: no visible global function definition for
  'complete.cases'
nodeplotboot : <anonymous>: no visible binding for global variable 'x'
nodeplotboot : <anonymous>: no visible binding for global variable 'y'
nodeplotdefault : <anonymous>: no visible binding for global variable
  'x'
nodeplotdefault : <anonymous>: no visible binding for global variable
  'y'
nodeplotdefault : <anonymous>: no visible binding for global variable
  'label'
ordinate: no visible global function definition for 'as.formula'
plot_clusgap: no visible binding for global variable 'k'
plot_clusgap: no visible binding for global variable 'gap'
plot_clusgap: no visible binding for global variable 'SE.sim'
plot_heatmap: no visible global function definition for
  'capture.output'
plot_heatmap: no visible binding for global variable 'Sample'
plot_heatmap: no visible binding for global variable 'OTU'
plot_heatmap: no visible binding for global variable 'Abundance'
plot_net : vertex_layout: no visible binding for global variable 'x'
plot_net : link_layout: no visible binding for global variable 'x'
plot_net : link_layout: no visible binding for global variable 'y'
plot_net: no visible binding for global variable 'x'
plot_net: no visible binding for global variable 'y'
plot_net: no visible binding for global variable 'xend'
plot_net: no visible binding for global variable 'yend'
plot_network: no visible binding for global variable 'x'
plot_network: no visible binding for global variable 'y'
plot_richness: no visible binding for global variable 'value'
plot_richness: no visible binding for global variable 'se'
plot_scree: no visible binding for global variable 'axis'
plot_scree: no visible binding for global variable 'eigenvalue'
plot_tree: no visible binding for global variable 'xleft'
plot_tree: no visible binding for global variable 'xright'
plot_tree: no visible binding for global variable 'y'
plot_tree: no visible binding for global variable 'x'
plot_tree: no visible binding for global variable 'vmin'
plot_tree: no visible binding for global variable 'vmax'
plot_tree: no visible binding for global variable 'OTU'
plot_tree: no visible binding for global variable 'label'
plot_tree: no visible binding for global variable 'Abundance'
plot_tree: no visible binding for global variable 'Sample'
plot_tree: no visible global function definition for ':='
plot_tree: no visible binding for global variable 'h.adj.index'
plot_tree: no visible binding for global variable 'xdodge'
plot_tree: no visible binding for global variable 'xfartiplab'
plot_tree: no visible binding for global variable '.SD'
rp.joint.fill: no visible global function definition for 'relevel'
tip_glom: no visible global function definition for 'as.dist'
tip_glom: no visible global function definition for 'cutree'
tip_glom: no visible global function definition for 'as.hclust'
tree_layout: no visible global function definition for ':='
tree_layout: no visible binding for global variable 'OTU'
tree_layout: no visible binding for global variable 'V2'
tree_layout: no visible binding for global variable 'xleft'
tree_layout: no visible binding for global variable 'V1'
tree_layout: no visible binding for global variable 'xright'
tree_layout: no visible binding for global variable 'y'
tree_layout: no visible binding for global variable 'x'
tree_layout: no visible binding for global variable 'label'
tree_layout: no visible global function definition for 'J'
tree_layout: no visible binding for global variable 'vmin'
tree_layout: no visible binding for global variable 'vmax'
JSD,matrix: no visible global function definition for 'combn'
JSD,matrix: no visible binding for global variable 'i'
JSD,matrix: no visible global function definition for 'as.dist'
capscale.phyloseq,phyloseq-formula-character: no visible global
  function definition for 'as.formula'
capscale.phyloseq,phyloseq-formula-dist: no visible global function
  definition for 'as.formula'
cca.phyloseq,phyloseq-formula: no visible global function definition
  for 'as.formula'
distance,phyloseq-character: no visible global function definition for
  'as.dist'
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
  binding for global variable 'X0'
merge_samples,sample_data: no visible global function definition for
  'aggregate'
plot_phyloseq,phyloseq: no visible binding for global variable
  'esophagus'
Undefined global functions or variables:
  #OTU ID .SD := Abundance Classification Consensus Lineage J OTU
  OTULabel SE.sim Sample V1 V2 X0 aggregate as.dist as.formula
  as.hclust axis capture.output combn complete.cases count cutree
  dcast.data.table download.file eigenvalue esophagus gap h.adj.index
  head i k label queryID queryString read read.table relevel se tail
  untar unzip value vmax vmin write.table x xdodge xend xfartiplab
  xleft xright y yend
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "aggregate", "as.dist", "as.formula", "as.hclust",
             "complete.cases", "cutree", "relevel")
  importFrom("utils", "capture.output", "combn", "download.file", "head",
             "read.table", "tail", "untar", "unzip", "write.table")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-phyloseq.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat-phyloseq.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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/phyloseq.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/phyloseq_1.38.0.tar.gz && rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL phyloseq_1.38.0.zip && rm phyloseq_1.38.0.tar.gz phyloseq_1.38.0.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 1738k  100 1738k    0     0  2562k      0 --:--:-- --:--:-- --:--:-- 2567k

install for i386

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

    access                                  html  
    assign-otu_table                        html  
    assign-phy_tree                         html  
    assign-sample_data                      html  
    assign-sample_names                     html  
    assign-tax_table                        html  
    assign-taxa_are_rows                    html  
    assign-taxa_names                       html  
    build_tax_table                         html  
    capscale-phyloseq-methods               html  
    cca-rda-phyloseq-methods                html  
    chunkReOrder                            html  
    data-GlobalPatterns                     html  
    data-enterotype                         html  
    data-esophagus                          html  
    data-soilrep                            html  
    decorana                                html  
    dist-class                              html  
    distance                                html  
    distanceMethodList                      html  
    envHash2otu_table                       html  
    estimate_richness                       html  
    export_env_file                         html  
    export_mothur_dist                      html  
    extract-methods                         html  
    filter_taxa                             html  
    filterfun_sample                        html  
    fix_phylo                               html  
    gapstat_ord                             html  
    genefilter_sample-methods               html  
    get.component.classes                   html  
    get_sample-methods                      html  
    get_taxa-methods                        html  
    get_taxa_unique                         html  
    get_variable                            html  
    getslots.phyloseq                       html  
    import                                  html  
    import_RDP_cluster                      html  
    import_RDP_otu                          html  
    import_biom                             html  
    import_env_file                         html  
    import_mothur                           html  
    import_mothur_constaxonomy              html  
    import_mothur_dist                      html  
    import_mothur_groups                    html  
    import_mothur_otu_table                 html  
    import_mothur_otulist                   html  
    import_mothur_shared                    html  
    import_pyrotagger_tab                   html  
    import_qiime                            html  
    import_qiime_otu_tax                    html  
    import_qiime_sample_data                html  
    import_uparse                           html  
    import_usearch_uc                       html  
    index_reorder                           html  
    intersect_taxa                          html  
    make_network                            html  
    merge_phyloseq                          html  
    merge_phyloseq_pair-methods             html  
    merge_samples-methods                   html  
    merge_taxa-methods                      html  
    metaMDS                                 html  
    microbio_me_qiime                       html  
    mt-methods                              html  
    nodeplotblank                           html  
    nodeplotboot                            html  
    nodeplotdefault                         html  
    nsamples-methods                        html  
    ntaxa-methods                           html  
    ordinate                                html  
    otu_table-class                         html  
    otu_table-methods                       html  
    parseTaxonomy-functions                 html  
    pcoa                                    html  
    phy_tree-methods                        html  
    phylo-class                             html  
    phylo                                   html  
    phyloseq-class                          html  
    phyloseq-deprecated                     html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/phyloseq.buildbin-libdir/00LOCK-phyloseq/00new/phyloseq/help/taxTab.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/phyloseq.buildbin-libdir/00LOCK-phyloseq/00new/phyloseq/help/speciesAreRows.html
    phyloseq-package                        html  
    phyloseq                                html  
    phyloseq_to_deseq2                      html  
    phyloseq_to_metagenomeSeq               html  
    plot_bar                                html  
    plot_clusgap                            html  
    plot_heatmap                            html  
    plot_net                                html  
    plot_network                            html  
    plot_ordination                         html  
    plot_phyloseq-methods                   html  
    plot_richness                           html  
    plot_scree                              html  
    plot_tree                               html  
    prune_samples-methods                   html  
    prune_taxa-methods                      html  
    psmelt                                  html  
    rank_names                              html  
    rarefy_even_depth                       html  
    read_tree                               html  
    read_tree_greengenes                    html  
    reconcile_categories                    html  
    refseq-methods                          html  
    rm_outlierf                             html  
    sample_data-class                       html  
    sample_data-methods                     html  
    sample_names-methods                    html  
    sample_sums                             html  
    sample_variables                        html  
    show-methods                            html  
    show_mothur_cutoffs                     html  
    splat.phyloseq.objects                  html  
    subset_ord_plot                         html  
    subset_samples-methods                  html  
    subset_taxa-methods                     html  
    tax_glom                                html  
    tax_table-methods                       html  
    taxa_are_rows-methods                   html  
    taxa_names-methods                      html  
    taxa_sums                               html  
    taxonomyTable-class                     html  
    threshrank                              html  
    threshrankfun                           html  
    tip_glom                                html  
    topf                                    html  
    topk                                    html  
    topp                                    html  
    transformcounts                         html  
    transpose-methods                       html  
    tree_layout                             html  
** building package indices
** installing vignettes
   'phyloseq-FAQ.Rmd' using 'UTF-8' 
   'phyloseq-analysis.Rmd' 
   'phyloseq-basics.Rmd' 
   'phyloseq-mixture-models.Rmd' 
** 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 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.38.0.zip
* DONE (phyloseq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'phyloseq' successfully unpacked and MD5 sums checked


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")
> packageVersion("phyloseq")
[1] '1.38.0'
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("phyloseq")
Loading required package: phyloseq
Found biom-format file, now parsing it... 
Done parsing biom... 
Importing Sample Metdadata from mapping file...
Merging the imported objects... 
Successfully merged, phyloseq-class created. 
 Returning... 
Found biom-format file, now parsing it... 
Done parsing biom... 
Importing Sample Metdadata from mapping file...
Merging the imported objects... 
Successfully merged, phyloseq-class created. 
 Returning... 
Reading `ucfile` into memory and parsing into table 
Initially read 100 entries. 
... Now removing unassigned OTUs (* or NA)... 
Removed 7 entries that had no OTU assignment. 
A total of 93 will be assigned to the OTU table.
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
Processing phylogenetic tree...
 C:/Users/biocbuild/bbs-3.14-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
Processing phylogenetic tree...
 C:/Users/biocbuild/bbs-3.14-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
[ FAIL 0 | WARN 49 | SKIP 0 | PASS 604 ]

[ FAIL 0 | WARN 49 | SKIP 0 | PASS 604 ]
> 
> proc.time()
   user  system elapsed 
  57.12    1.39   58.67


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")
> packageVersion("phyloseq")
[1] '1.38.0'
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("phyloseq")
Loading required package: phyloseq
Found biom-format file, now parsing it... 
Done parsing biom... 
Importing Sample Metdadata from mapping file...
Merging the imported objects... 
Successfully merged, phyloseq-class created. 
 Returning... 
Found biom-format file, now parsing it... 
Done parsing biom... 
Importing Sample Metdadata from mapping file...
Merging the imported objects... 
Successfully merged, phyloseq-class created. 
 Returning... 
Reading `ucfile` into memory and parsing into table 
Initially read 100 entries. 
... Now removing unassigned OTUs (* or NA)... 
Removed 7 entries that had no OTU assignment. 
A total of 93 will be assigned to the OTU table.
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
Processing phylogenetic tree...
 C:/Users/biocbuild/bbs-3.14-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
Processing phylogenetic tree...
 C:/Users/biocbuild/bbs-3.14-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
[ FAIL 0 | WARN 49 | SKIP 0 | PASS 604 ]

[ FAIL 0 | WARN 49 | SKIP 0 | PASS 604 ]
> 
> proc.time()
   user  system elapsed 
  62.40    1.00   63.45

name	user	system	elapsed
DPCoA	1.87	0.19	2.07
JSD	0	0	0
UniFrac-methods	0.08	0.01	0.10
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.04	0.00	0.04
assign-sample_data	0.11	0.02	0.13
assign-sample_names	0.02	0.00	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.02	0.00	0.02
build_tax_table	0.01	0.00	0.01
capscale-phyloseq-methods	0.66	0.02	0.68
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.47	0.01	1.48
data-enterotype	1.06	0.00	1.06
data-esophagus	0.44	0.03	0.53
data-soilrep	1.29	0.06	1.36
distance	0.24	0.05	0.44
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.07	0.02	0.08
extract-methods	0.00	0.01	0.01
filter_taxa	1.01	0.07	1.08
filterfun_sample	0.02	0.00	0.02
gapstat_ord	1.67	0.03	1.70
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.02	0.00	0.01
get_taxa-methods	0	0	0
get_taxa_unique	0.23	0.01	0.25
get_variable	0.20	0.00	0.21
getslots.phyloseq	0.21	0.02	0.22
import	0	0	0
import_RDP_otu	1.32	0.01	1.51
import_biom	0.16	0.00	0.16
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.73	0.00	0.82
import_qiime_otu_tax	0.83	0.02	0.84
import_qiime_sample_data	0	0	0
import_uparse	0	0	0
import_usearch_uc	0.03	0.01	0.08
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.25	0.04	2.28
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.56	0.04	0.61
merge_taxa-methods	0.04	0.00	0.05
microbio_me_qiime	0.68	0.00	1.52
mt-methods	1.47	0.00	1.47
nodeplotblank	0.29	0.02	0.31
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.01	0.00	0.02
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.26	0.00	0.27
phyloseq	0.02	0.00	0.02
phyloseq_to_deseq2	3.27	0.03	3.29
phyloseq_to_metagenomeSeq	1.14	0.08	1.22
plot_bar	1.40	0.12	1.53
plot_clusgap	3.08	0.28	3.41
plot_heatmap	2.52	0.30	2.81
plot_net	2.89	0.25	3.14
plot_network	1.59	0.02	1.61
plot_ordination	0.50	0.04	0.55
plot_phyloseq-methods	0.17	0.00	0.17
plot_richness	3.39	0.05	3.44
plot_scree	1.18	0.06	1.23
plot_tree	0.42	0.00	0.42
prune_samples-methods	0.39	0.03	0.43
prune_taxa-methods	0.04	0.00	0.04
psmelt	0.6	0.0	0.6
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.06	0.00	0.06
read_tree	0.02	0.00	0.02
read_tree_greengenes	0.01	0.00	0.01
reconcile_categories	0	0	0
refseq-methods	0.21	0.00	0.20
rm_outlierf	0.01	0.00	0.02
sample_data-methods	0.06	0.00	0.06
sample_names-methods	0.02	0.00	0.02
sample_sums	0.03	0.00	0.03
sample_variables	0.05	0.00	0.05
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.01	0.00	0.01
taxa_sums	0.05	0.00	0.05
threshrank	1.81	0.52	2.33
threshrankfun	0.05	0.00	0.05
tip_glom	0.54	0.00	0.55
topf	0	0	0
topk	0.02	0.00	0.01
topp	0.01	0.00	0.02
transformcounts	0.08	0.00	0.08
transpose-methods	0.75	0.33	1.07
tree_layout	0.46	0.01	0.47

name	user	system	elapsed
DPCoA	2.60	0.08	2.67
JSD	0	0	0
UniFrac-methods	0.1	0.0	0.1
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.03	0.00	0.03
assign-sample_data	0.09	0.03	0.12
assign-sample_names	0	0	0
assign-tax_table	0	0	0
assign-taxa_are_rows	0.00	0.02	0.02
assign-taxa_names	0	0	0
build_tax_table	0.02	0.00	0.02
capscale-phyloseq-methods	0.53	0.00	0.53
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.33	0.00	1.32
data-enterotype	1.11	0.01	1.13
data-esophagus	0.51	0.00	0.52
data-soilrep	0.88	0.05	0.92
distance	0.31	0.02	0.33
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.05	0.00	0.04
export_env_file	0	0	0
export_mothur_dist	0.07	0.00	0.08
extract-methods	0.04	0.00	0.03
filter_taxa	1.69	0.01	1.70
filterfun_sample	0.03	0.00	0.03
gapstat_ord	1.22	0.03	1.25
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0	0	0
get_taxa_unique	0.21	0.00	0.20
get_variable	0.15	0.00	0.15
getslots.phyloseq	0.14	0.01	0.16
import	0	0	0
import_RDP_otu	0.75	0.00	0.75
import_biom	0.16	0.00	0.15
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.86	0.02	0.88
import_qiime_otu_tax	0.75	0.03	0.78
import_qiime_sample_data	0	0	0
import_uparse	0	0	0
import_usearch_uc	0.02	0.00	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.03	0.00	2.03
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.51	0.03	0.54
merge_taxa-methods	0.06	0.00	0.07
microbio_me_qiime	0.66	0.00	0.75
mt-methods	1.36	0.00	1.36
nodeplotblank	0.25	0.00	0.25
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.01
ntaxa-methods	0.00	0.02	0.02
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.15	0.00	0.15
phyloseq	0.02	0.00	0.02
phyloseq_to_deseq2	3.39	0.06	3.45
phyloseq_to_metagenomeSeq	1.00	0.09	1.09
plot_bar	2.39	0.10	2.49
plot_clusgap	2.72	0.03	2.81
plot_heatmap	2.41	0.02	2.42
plot_net	3.05	0.00	3.05
plot_network	1.67	0.00	1.67
plot_ordination	0.56	0.00	0.56
plot_phyloseq-methods	0.17	0.00	0.17
plot_richness	3.86	0.04	3.91
plot_scree	1.53	0.03	1.56
plot_tree	0.43	0.03	0.46
prune_samples-methods	0.33	0.00	0.33
prune_taxa-methods	0.04	0.00	0.03
psmelt	0.54	0.02	0.56
rank_names	0.02	0.00	0.01
rarefy_even_depth	0.08	0.00	0.08
read_tree	0.01	0.00	0.02
read_tree_greengenes	0	0	0
reconcile_categories	0	0	0
refseq-methods	0.13	0.03	0.15
rm_outlierf	0.01	0.00	0.02
sample_data-methods	0.05	0.00	0.05
sample_names-methods	0	0	0
sample_sums	0.01	0.00	0.02
sample_variables	0.03	0.00	0.03
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.02	0.00	0.02
taxa_sums	0.03	0.00	0.03
threshrank	2.28	0.37	2.66
threshrankfun	0.06	0.00	0.06
tip_glom	0.53	0.00	0.53
topf	0	0	0
topk	0.02	0.00	0.02
topp	0.02	0.00	0.01
transformcounts	0.07	0.00	0.08
transpose-methods	0.61	0.35	0.95
tree_layout	0.41	0.01	0.43

CHECK results for phyloseq on tokay2

Summary

Command output

Installation output

Tests output

Example timings