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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phyloseq_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/phyloseq.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.54.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
threshrank         3.655  4.452   8.851
plot_heatmap       7.781  0.198   9.291
phyloseq_to_deseq2 7.777  0.136   8.280
plot_richness      7.006  0.286   8.172
plot_net           6.948  0.141   7.962
DPCoA              5.734  0.295   6.228
plot_clusgap       5.185  0.138   6.077
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’
 ERROR
Running the tests in ‘tests/testthat-phyloseq.R’ failed.
Last 13 lines of output:
  ── Error ('test-subset.R:67:2'): The set of names should be the same after pruning, names(samobs) ──
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test-subset.R:67:9
  ── Error ('test-subset.R:74:2'): The set/order of taxa names after pruning should be consistent ──
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test-subset.R:74:9
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 550 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phyloseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘phyloseq’ ...
** this is package ‘phyloseq’ version ‘1.54.0’
** 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)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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] '1.54.0'
> # 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
Saving _problems/test-IO-48.R
Saving _problems/test-IO-155.R
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...
 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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...
 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
Saving _problems/test-phyloseq-54.R
Saving _problems/test-phyloseq-78.R
Saving _problems/test-phyloseq-114.R
Saving _problems/test-subset-58.R
Saving _problems/test-subset-67.R
Saving _problems/test-subset-74.R
[ FAIL 8 | WARN 2 | SKIP 0 | PASS 550 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-IO.R:48:2'): import_mothur: imported files become S4 object ────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(isS4(esophman), is_true()) at test-IO.R:48:9
── Error ('test-IO.R:155:2'): Taxonomy vector parsing functions behave as expected ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-IO.R:155:9
── Error ('test-phyloseq.R:54:2'): taxa_names(x)<- and sample_names(x)<- behaves as expected ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-phyloseq.R:54:9
── Error ('test-phyloseq.R:78:2'): Test intersect_*() and prune_*() methods behave as expected ──
Error in `is_false()`: could not find function "is_false"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-phyloseq.R:78:9
── Error ('test-phyloseq.R:114:2'): Test ordering ──────────────────────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-phyloseq.R:114:9
── Error ('test-subset.R:58:2'): Initial order before pruning check is different ──
Error in `is_false()`: could not find function "is_false"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-subset.R:58:9
── Error ('test-subset.R:67:2'): The set of names should be the same after pruning, names(samobs) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-subset.R:67:9
── Error ('test-subset.R:74:2'): The set/order of taxa names after pruning should be consistent ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test-subset.R:74:9

[ FAIL 8 | WARN 2 | SKIP 0 | PASS 550 ]
Error:
! Test failures.
Execution halted