Build/check report for BioC 3.22 - CHECK results for phyloseq on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4894
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 nebbiolo2

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: 1.54.2

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings phyloseq_1.54.2.tar.gz

StartedAt: 2026-03-05 02:45:34 -0500 (Thu, 05 Mar 2026)

EndedAt: 2026-03-05 02:51:27 -0500 (Thu, 05 Mar 2026)

EllapsedTime: 352.4 seconds

RetCode: 0

Status: OK

CheckDir: phyloseq.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings phyloseq_1.54.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/phyloseq.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.54.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 ... 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 ... 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

Installation output

phyloseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL phyloseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘phyloseq’ ...
** this is package ‘phyloseq’ version ‘1.54.2’
** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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] '1.54.2'
> # 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-3.22-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-3.22-bioc/R/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 604 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 604 ]
> 
> proc.time()
   user  system elapsed 
 57.398   1.301  58.650

Example timings

phyloseq.Rcheck/phyloseq-Ex.timings

name	user	system	elapsed
DPCoA	2.522	0.120	2.641
JSD	0	0	0
UniFrac-methods	0.073	0.001	0.074
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.029	0.000	0.030
assign-sample_data	0.092	0.001	0.093
assign-sample_names	0.005	0.001	0.006
assign-tax_table	0	0	0
assign-taxa_are_rows	0.002	0.000	0.001
assign-taxa_names	0.004	0.000	0.004
build_tax_table	0.008	0.000	0.008
capscale-phyloseq-methods	0.523	0.035	0.557
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0.000	0.000	0.001
data-GlobalPatterns	1.323	0.060	1.383
data-enterotype	0.758	0.007	0.765
data-esophagus	0.372	0.018	0.390
data-soilrep	1.209	0.034	1.243
distance	0.143	0.007	0.156
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.019	0.000	0.019
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.028	0.005	0.033
extract-methods	0.007	0.000	0.007
filter_taxa	0.931	0.018	0.949
filterfun_sample	0.013	0.000	0.013
gapstat_ord	1.243	0.012	1.255
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.001	0.001	0.003
get_taxa-methods	0.002	0.000	0.002
get_taxa_unique	0.203	0.005	0.209
get_variable	0.146	0.008	0.155
getslots.phyloseq	0.174	0.002	0.176
import	0	0	0
import_RDP_otu	0.258	0.000	0.258
import_biom	0.090	0.002	0.092
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	0.768	0.062	0.831
import_qiime_otu_tax	0.634	0.007	0.641
import_qiime_sample_data	0.007	0.000	0.006
import_uparse	0	0	0
import_usearch_uc	0.011	0.000	0.011
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	1.273	0.007	1.281
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	0.52	0.02	0.54
merge_taxa-methods	0.041	0.000	0.041
microbio_me_qiime	0.431	0.005	0.436
mt-methods	1.150	0.000	1.152
nodeplotblank	0.387	0.001	0.378
nodeplotboot	0.001	0.000	0.001
nodeplotdefault	0.001	0.000	0.000
nsamples-methods	0.017	0.000	0.017
ntaxa-methods	0.003	0.000	0.002
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0.001	0.000	0.001
phy_tree-methods	0.148	0.003	0.151
phyloseq	0.017	0.001	0.018
phyloseq_to_deseq2	3.701	0.055	3.756
phyloseq_to_metagenomeSeq	1.626	0.045	1.671
plot_bar	1.573	0.166	1.739
plot_clusgap	2.439	0.036	2.475
plot_heatmap	2.847	0.016	2.863
plot_net	3.714	0.022	3.620
plot_network	1.088	0.003	1.091
plot_ordination	0.479	0.006	0.485
plot_phyloseq-methods	0.243	0.000	0.237
plot_richness	3.728	0.034	3.762
plot_scree	1.483	0.005	1.489
plot_tree	0.582	0.000	0.571
prune_samples-methods	0.328	0.002	0.330
prune_taxa-methods	0.030	0.002	0.033
psmelt	0.622	0.002	0.624
rank_names	0.022	0.000	0.022
rarefy_even_depth	0.062	0.000	0.062
read_tree	0.013	0.000	0.013
read_tree_greengenes	0.008	0.001	0.008
reconcile_categories	0	0	0
refseq-methods	0.141	0.006	0.147
rm_outlierf	0.015	0.000	0.014
sample_data-methods	0.045	0.002	0.047
sample_names-methods	0.000	0.001	0.001
sample_sums	0.020	0.004	0.024
sample_variables	0.019	0.003	0.022
show-methods	0	0	0
splat.phyloseq.objects	0.001	0.000	0.000
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	0.016	0.000	0.016
taxa_sums	0.025	0.002	0.026
threshrank	1.177	0.183	1.360
threshrankfun	0.044	0.000	0.045
tip_glom	0.685	0.001	0.662
topf	0.01	0.00	0.01
topk	0.009	0.000	0.008
topp	0.008	0.000	0.008
transformcounts	0.066	0.001	0.067
transpose-methods	0.372	0.144	0.516
tree_layout	0.610	0.001	0.589