Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:06:46 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 phyloseq on tokay2


To the developers/maintainers of the phyloseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phyloseq.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 1415/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.38.0  (landing page)
Paul J. McMurdie
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/phyloseq
git_branch: RELEASE_3_14
git_last_commit: 1e2409a
git_last_commit_date: 2021-10-26 12:01:53 -0500 (Tue, 26 Oct 2021)
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: 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: 2022-01-17 01:27:03 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 01:34:31 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 447.5 seconds
RetCode: 0
Status:   OK  
CheckDir: phyloseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.1.2 (2021-11-01)
* 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.



Installation output

phyloseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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  4555k      0 --:--:-- --:--:-- --:--:-- 4561k

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

Tests output

phyloseq.Rcheck/tests_i386/testthat-phyloseq.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
> 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 ]
> 
> proc.time()
   user  system elapsed 
  55.71    1.57   57.50 

phyloseq.Rcheck/tests_x64/testthat-phyloseq.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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")
> 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 ]
> 
> proc.time()
   user  system elapsed 
  58.75    0.92   59.78 

Example timings

phyloseq.Rcheck/examples_i386/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA2.110.512.62
JSD000
UniFrac-methods0.100.000.09
access000
assign-otu_table000
assign-phy_tree0.050.000.05
assign-sample_data0.100.000.11
assign-sample_names0.000.020.01
assign-tax_table000
assign-taxa_are_rows000
assign-taxa_names000
build_tax_table0.020.000.02
capscale-phyloseq-methods0.540.020.56
cca-rda-phyloseq-methods000
chunkReOrder000
data-GlobalPatterns1.170.041.22
data-enterotype0.930.000.92
data-esophagus0.700.001.09
data-soilrep1.720.071.78
distance0.260.042.00
distanceMethodList000
envHash2otu_table000
estimate_richness0.040.020.05
export_env_file000
export_mothur_dist0.090.000.09
extract-methods0.020.000.02
filter_taxa1.190.001.18
filterfun_sample0.010.000.02
gapstat_ord1.220.011.24
genefilter_sample-methods000
get.component.classes000
get_sample-methods000
get_taxa-methods000
get_taxa_unique0.270.000.27
get_variable0.20.00.2
getslots.phyloseq0.170.030.21
import000
import_RDP_otu1.680.001.92
import_biom0.230.020.25
import_env_file000
import_mothur000
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.720.000.74
import_qiime_otu_tax0.660.010.67
import_qiime_sample_data0.010.000.02
import_uparse000
import_usearch_uc000
index_reorder000
intersect_taxa000
make_network1.860.001.86
merge_phyloseq000
merge_phyloseq_pair-methods000
merge_samples-methods0.530.050.58
merge_taxa-methods0.040.000.05
microbio_me_qiime0.740.000.93
mt-methods1.730.031.80
nodeplotblank0.250.000.27
nodeplotboot000
nodeplotdefault000
nsamples-methods0.020.020.03
ntaxa-methods000
ordinate000
otu_table-methods000
parseTaxonomy-functions0.010.000.01
phy_tree-methods0.210.000.21
phyloseq0.010.000.01
phyloseq_to_deseq23.170.063.24
phyloseq_to_metagenomeSeq1.070.081.14
plot_bar1.470.211.68
plot_clusgap3.500.133.74
plot_heatmap2.230.022.25
plot_net2.860.032.89
plot_network1.610.011.62
plot_ordination0.550.050.60
plot_phyloseq-methods0.170.000.17
plot_richness3.280.053.33
plot_scree1.120.011.14
plot_tree0.390.000.39
prune_samples-methods0.400.000.39
prune_taxa-methods0.030.000.03
psmelt0.560.000.56
rank_names0.030.000.03
rarefy_even_depth0.060.000.06
read_tree0.020.000.02
read_tree_greengenes000
reconcile_categories000
refseq-methods0.190.010.20
rm_outlierf0.010.000.02
sample_data-methods0.060.000.06
sample_names-methods000
sample_sums0.050.000.05
sample_variables0.030.000.03
show-methods000
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom000
tax_table-methods000
taxa_names-methods0.020.000.01
taxa_sums0.040.000.05
threshrank2.430.502.92
threshrankfun0.030.020.05
tip_glom0.500.000.52
topf000
topk000
topp0.020.000.02
transformcounts0.080.000.07
transpose-methods0.700.270.97
tree_layout0.330.000.33

phyloseq.Rcheck/examples_x64/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA1.970.032.00
JSD000
UniFrac-methods0.090.000.10
access000
assign-otu_table000
assign-phy_tree0.030.000.03
assign-sample_data0.100.010.11
assign-sample_names0.010.000.01
assign-tax_table000
assign-taxa_are_rows000
assign-taxa_names000
build_tax_table0.020.000.02
capscale-phyloseq-methods0.500.020.51
cca-rda-phyloseq-methods000
chunkReOrder000
data-GlobalPatterns1.230.011.25
data-enterotype1.140.031.18
data-esophagus0.690.020.70
data-soilrep1.340.021.36
distance0.160.040.20
distanceMethodList000
envHash2otu_table000
estimate_richness0.030.000.03
export_env_file000
export_mothur_dist0.030.020.05
extract-methods000
filter_taxa1.490.031.51
filterfun_sample0.010.000.02
gapstat_ord1.250.021.26
genefilter_sample-methods000
get.component.classes000
get_sample-methods000
get_taxa-methods000
get_taxa_unique0.160.050.21
get_variable0.160.000.15
getslots.phyloseq0.140.010.16
import000
import_RDP_otu0.760.000.76
import_biom0.160.020.18
import_env_file000
import_mothur000
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.840.010.85
import_qiime_otu_tax0.700.040.74
import_qiime_sample_data0.020.000.01
import_uparse000
import_usearch_uc0.020.000.02
index_reorder000
intersect_taxa000
make_network1.980.001.98
merge_phyloseq000
merge_phyloseq_pair-methods000
merge_samples-methods0.540.000.55
merge_taxa-methods0.050.000.04
microbio_me_qiime0.750.001.00
mt-methods1.690.001.74
nodeplotblank0.370.000.47
nodeplotboot0.020.000.01
nodeplotdefault000
nsamples-methods0.030.000.03
ntaxa-methods000
ordinate000
otu_table-methods000
parseTaxonomy-functions000
phy_tree-methods0.200.010.22
phyloseq0.030.000.03
phyloseq_to_deseq23.530.063.60
phyloseq_to_metagenomeSeq0.960.031.04
plot_bar2.510.042.55
plot_clusgap2.750.112.95
plot_heatmap2.380.012.40
plot_net4.170.024.18
plot_network1.660.001.66
plot_ordination0.500.030.53
plot_phyloseq-methods0.150.010.17
plot_richness3.740.103.83
plot_scree1.560.041.61
plot_tree0.440.000.44
prune_samples-methods0.330.070.39
prune_taxa-methods0.040.000.04
psmelt0.600.010.61
rank_names0.010.000.02
rarefy_even_depth0.110.020.12
read_tree0.030.000.04
read_tree_greengenes0.000.000.01
reconcile_categories000
refseq-methods0.260.000.26
rm_outlierf0.030.000.03
sample_data-methods0.080.000.08
sample_names-methods000
sample_sums0.050.000.05
sample_variables0.050.000.05
show-methods000
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom000
tax_table-methods000
taxa_names-methods0.030.010.04
taxa_sums0.030.020.05
threshrank1.940.472.41
threshrankfun0.060.000.06
tip_glom0.910.000.90
topf0.010.000.02
topk0.020.000.02
topp0.020.000.02
transformcounts0.150.000.15
transpose-methods0.930.581.50
tree_layout0.620.000.63