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This page was generated on 2024-10-24 11:04 -0400 (Thu, 24 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 3656
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Package 1543/2281HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.49.0  (landing page)
Paul J. McMurdie
Snapshot Date: 2024-10-23 19:16 -0400 (Wed, 23 Oct 2024)
git_url: https://git.bioconductor.org/packages/phyloseq
git_branch: devel
git_last_commit: 6bb7e90
git_last_commit_date: 2024-04-30 10:26:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  

CHECK results for phyloseq on nebbiolo1

To the developers/maintainers of the phyloseq package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: phyloseq
Version: 1.49.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings phyloseq_1.49.0.tar.gz
StartedAt: 2024-10-24 08:57:21 -0400 (Thu, 24 Oct 2024)
EndedAt: 2024-10-24 09:02:35 -0400 (Thu, 24 Oct 2024)
EllapsedTime: 314.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: phyloseq.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings phyloseq_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.49.0’
* 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 for sufficient/correct file permissions ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... WARNING
checkRd: (-1) import_biom.Rd:15: Lost braces
    15 | \url{http://www.qiime.org/svn_documentation/documentation/biom_format.html}{the biom-format home page}.
       |                                                                            ^
checkRd: (-1) import_biom.Rd:45: Lost braces
    45 | as in the case of the GreenGenes tree mentioned earlier (code{\link{read_tree_greengenes}}).}
       |                                                              ^
checkRd: (-1) import_biom.Rd:92: Lost braces
    92 | \url{http://greengenes.lbl.gov/cgi-bin/nph-index.cgi}{greengenes},
       |                                                      ^
checkRd: (-1) import_pyrotagger_tab.Rd:55: Lost braces
    55 | \code{R}. Rather than add to the dependency requirements of emph{phyloseq}
       |                                                                 ^
checkRd: (-1) import_qiime.Rd:44: Lost braces
    44 | as in the case of the GreenGenes tree mentioned earlier (code{\link{read_tree_greengenes}}).}
       |                                                              ^
checkRd: (7) import_qiime.Rd:120: Invalid URL: "http://www.qiime.org/"
checkRd: (-1) merge_samples-methods.Rd:71: Lost braces
    71 | \code{\link{merge_taxa}}, code{\link{merge_phyloseq}}
       |                               ^
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'phyloseq-deprecated.Rd':
  ‘phyloseq-deprecated-package’
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  UniFrac-methods.Rd: foreach-package
  distance.Rd: designdist
  import_biom.Rd: foreach
  import_qiime_otu_tax.Rd: foreach-package
  import_uparse.Rd: data.table
  ordinate.Rd: cca, rda
  phyloseq.Rd: ape-package
  plot_bar.Rd: melt, ggplot, qplot
  plot_heatmap.Rd: log_trans, ggplot
  plot_net.Rd: igraph-package, ggplot, ggsave
  plot_network.Rd: ggplot
  plot_ordination.Rd: ggplot
  plot_richness.Rd: ggplot
  plot_scree.Rd: ggplot
  plot_tree.Rd: ape, ggplot, plot.phylo
  subset_ord_plot.Rd: ggplot
  tree_layout.Rd: data.table, ape-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in Rd file 'cca-rda-phyloseq-methods.Rd':
  ‘cca.phyloseq’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘phyloseq-FAQ.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-FAQ_files/figure-html/unnamed-chunk-2-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-FAQ_files/figure-html/unnamed-chunk-3-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-FAQ_files/figure-html/unnamed-chunk-3-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-FAQ_files/figure-html/unnamed-chunk-4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-FAQ_files/figure-html/unnamed-chunk-4-2.png" but not available.
--- finished re-building ‘phyloseq-FAQ.Rmd’

--- re-building ‘phyloseq-analysis.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/richness_estimates0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/richness_estimates-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GP-chl-tree-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/EntAbundPlot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/entbarplot0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPheatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPheatmap-rename-axes-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/plot_sample_network-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/PCoAScree-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPfig5ax1213-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPfig5ax1213-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GP_UF_NMDS0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPCAscree-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPCA1234-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPCA1234-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPCAspecplot0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPCAspecplotTopo0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPCAjitter0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPtaxaplot0-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPdpcoa01-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPdpcoa02-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPdpcoa02-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/GPdpcoa02-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-analysis_files/figure-html/unnamed-chunk-12-1.png" but not available.
--- finished re-building ‘phyloseq-analysis.Rmd’

--- re-building ‘phyloseq-basics.Rmd’ using rmarkdown
YAML parse exception at line 2, column 6,
while scanning a block scalar:
did not find expected comment or line break
Error: processing vignette 'phyloseq-basics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 64
--- failed re-building ‘phyloseq-basics.Rmd’

--- re-building ‘phyloseq-mixture-models.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/vign_test/phyloseq/vignettes/phyloseq-mixture-models_files/figure-html/bar-plot-1.png" but not available.
--- finished re-building ‘phyloseq-mixture-models.Rmd’

SUMMARY: processing the following file failed:
  ‘phyloseq-basics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

Installation output

phyloseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL phyloseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘phyloseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (phyloseq)

Tests output

phyloseq.Rcheck/tests/testthat-phyloseq.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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] '1.49.0'
> # 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...
 /home/biocbuild/bbs-3.21-bioc/R/site-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...
 /home/biocbuild/bbs-3.21-bioc/R/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
[ FAIL 0 | WARN 51 | SKIP 0 | PASS 604 ]

[ FAIL 0 | WARN 51 | SKIP 0 | PASS 604 ]
> 
> proc.time()
   user  system elapsed 
 48.903   0.966  49.824

Example timings

phyloseq.Rcheck/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA1.5310.1231.654
JSD000
UniFrac-methods0.0760.0010.077
access000
assign-otu_table000
assign-phy_tree0.0280.0020.029
assign-sample_data0.0870.0050.093
assign-sample_names0.0060.0000.006
assign-tax_table000
assign-taxa_are_rows0.0010.0010.002
assign-taxa_names0.0050.0000.005
build_tax_table0.0080.0000.008
capscale-phyloseq-methods0.5000.0310.531
cca-rda-phyloseq-methods0.0010.0000.000
chunkReOrder000
data-GlobalPatterns1.1710.0481.220
data-enterotype0.6130.0030.616
data-esophagus0.3830.0020.384
data-soilrep1.0390.0251.065
distance0.1510.0120.164
distanceMethodList0.0000.0000.001
envHash2otu_table000
estimate_richness0.0160.0020.018
export_env_file000
export_mothur_dist0.0230.0330.056
extract-methods0.0050.0010.006
filter_taxa0.8810.0130.894
filterfun_sample0.0130.0000.013
gapstat_ord1.7260.0681.794
genefilter_sample-methods000
get.component.classes000
get_sample-methods0.0010.0020.002
get_taxa-methods0.0010.0010.002
get_taxa_unique0.1750.0180.193
get_variable0.1370.0060.144
getslots.phyloseq0.1390.0070.146
import000
import_RDP_otu0.2580.0020.260
import_biom0.1140.0000.115
import_env_file0.0000.0000.001
import_mothur0.0010.0000.000
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.7140.0660.780
import_qiime_otu_tax0.6650.1060.771
import_qiime_sample_data0.0070.0010.008
import_uparse0.0000.0000.001
import_usearch_uc0.0080.0100.018
index_reorder000
intersect_taxa000
make_network1.1100.0061.116
merge_phyloseq000
merge_phyloseq_pair-methods0.0000.0010.000
merge_samples-methods0.5120.0400.551
merge_taxa-methods0.0400.0010.041
microbio_me_qiime0.3830.0060.390
mt-methods1.2890.0021.291
nodeplotblank0.2660.0020.258
nodeplotboot0.0010.0010.001
nodeplotdefault0.0010.0000.000
nsamples-methods0.0150.0010.015
ntaxa-methods0.0020.0010.002
ordinate000
otu_table-methods0.0000.0010.000
parseTaxonomy-functions0.0010.0010.002
phy_tree-methods0.1390.0090.148
phyloseq0.0160.0000.016
phyloseq_to_deseq23.3980.1173.514
phyloseq_to_metagenomeSeq1.5160.0961.613
plot_bar1.2550.0531.308
plot_clusgap2.2180.0322.249
plot_heatmap2.2340.0602.294
plot_net3.1190.0113.033
plot_network0.8920.0390.932
plot_ordination0.4310.0120.444
plot_phyloseq-methods0.1610.0000.155
plot_richness3.0610.0513.114
plot_scree1.2080.0121.221
plot_tree0.4140.0010.387
prune_samples-methods0.3380.0030.342
prune_taxa-methods0.0300.0020.032
psmelt0.4880.0070.496
rank_names0.0210.0000.021
rarefy_even_depth0.0570.0010.058
read_tree0.0110.0010.013
read_tree_greengenes0.0080.0010.008
reconcile_categories0.0000.0000.001
refseq-methods0.1380.0050.143
rm_outlierf0.0130.0020.014
sample_data-methods0.0560.0030.060
sample_names-methods0.0020.0000.002
sample_sums0.0220.0060.028
sample_variables0.0210.0010.022
show-methods0.0000.0000.001
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods0.0000.0000.001
subset_taxa-methods000
tax_glom0.0010.0000.000
tax_table-methods0.0000.0000.001
taxa_names-methods0.0170.0020.019
taxa_sums0.0270.0110.037
threshrank1.2021.7252.926
threshrankfun0.0370.0040.041
tip_glom0.5390.0090.517
topf0.0090.0000.010
topk0.0070.0010.008
topp0.0080.0000.008
transformcounts0.0610.0030.065
transpose-methods0.4191.2201.639
tree_layout0.4230.0070.400