Multiple platform build/check report for BioC 3.16 - CHECK results for phyloseq on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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*

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings phyloseq_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/phyloseq.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.42.0’
* 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 R 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plot_richness 7.183  0.184   7.384
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 ...
  ‘phyloseq-FAQ.Rmd’ using ‘UTF-8’... OK
  ‘phyloseq-analysis.Rmd’... OK
  ‘phyloseq-basics.Rmd’... OK
  ‘phyloseq-mixture-models.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

Installation output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL phyloseq
###
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* installing to library ‘/home/biocbuild/bbs-3.16-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


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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] '1.42.0'
> # 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-3.16-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-3.16-bioc/R/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
[ FAIL 0 | WARN 49 | SKIP 0 | PASS 604 ]

[ FAIL 0 | WARN 49 | SKIP 0 | PASS 604 ]
> 
> proc.time()
   user  system elapsed 
100.948   3.482 111.976

Example timings

name	user	system	elapsed
DPCoA	2.234	0.088	2.322
JSD	0	0	0
UniFrac-methods	0.081	0.004	0.085
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.044	0.004	0.047
assign-sample_data	0.099	0.004	0.103
assign-sample_names	0.006	0.000	0.006
assign-tax_table	0	0	0
assign-taxa_are_rows	0.001	0.000	0.002
assign-taxa_names	0.004	0.000	0.005
build_tax_table	0.009	0.000	0.009
capscale-phyloseq-methods	1.201	0.092	1.293
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.383	0.020	1.402
data-enterotype	0.723	0.032	0.755
data-esophagus	0.389	0.000	0.390
data-soilrep	0.845	0.024	0.922
distance	0.212	0.012	0.261
distanceMethodList	0.001	0.000	0.000
envHash2otu_table	0	0	0
estimate_richness	0.038	0.008	0.078
export_env_file	0	0	0
export_mothur_dist	0.065	0.008	0.076
extract-methods	0.016	0.003	0.020
filter_taxa	2.082	0.038	2.666
filterfun_sample	0.035	0.000	0.035
gapstat_ord	2.199	0.036	3.147
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.008	0.004	0.012
get_taxa-methods	0.002	0.004	0.005
get_taxa_unique	0.320	0.008	0.506
get_variable	0.267	0.004	0.352
getslots.phyloseq	0.323	0.008	0.551
import	0	0	0
import_RDP_otu	1.706	0.107	3.557
import_biom	0.320	0.008	0.456
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	1.875	0.052	3.417
import_qiime_otu_tax	1.815	0.083	2.519
import_qiime_sample_data	0.014	0.004	0.018
import_uparse	0	0	0
import_usearch_uc	0.028	0.000	0.058
index_reorder	0	0	0
intersect_taxa	0.001	0.000	0.001
make_network	3.036	0.024	3.386
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	0.762	0.044	0.806
merge_taxa-methods	0.075	0.004	0.079
microbio_me_qiime	1.063	0.010	1.073
mt-methods	1.397	0.004	1.402
nodeplotblank	0.284	0.008	0.278
nodeplotboot	0.001	0.000	0.001
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.02
ntaxa-methods	0.003	0.000	0.003
ordinate	0.001	0.000	0.000
otu_table-methods	0	0	0
parseTaxonomy-functions	0.002	0.000	0.001
phy_tree-methods	0.143	0.004	0.146
phyloseq	0.019	0.000	0.019
phyloseq_to_deseq2	3.409	0.120	3.529
phyloseq_to_metagenomeSeq	0.849	0.064	0.913
plot_bar	1.808	0.115	1.991
plot_clusgap	3.275	0.117	3.392
plot_heatmap	2.382	0.064	2.446
plot_net	3.187	0.011	3.200
plot_network	1.131	0.008	1.139
plot_ordination	1.016	0.016	1.033
plot_phyloseq-methods	0.417	0.005	0.416
plot_richness	7.183	0.184	7.384
plot_scree	2.877	0.068	3.470
plot_tree	1.144	0.028	1.171
prune_samples-methods	0.648	0.020	0.669
prune_taxa-methods	0.073	0.000	0.073
psmelt	1.222	0.016	1.305
rank_names	0.027	0.004	0.031
rarefy_even_depth	0.154	0.000	0.153
read_tree	0.018	0.004	0.022
read_tree_greengenes	0.016	0.000	0.015
reconcile_categories	0	0	0
refseq-methods	0.231	0.008	0.239
rm_outlierf	0.043	0.000	0.044
sample_data-methods	0.090	0.008	0.097
sample_names-methods	0.003	0.000	0.004
sample_sums	0.033	0.004	0.037
sample_variables	0.029	0.004	0.032
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.047	0.012	0.059
taxa_sums	0.039	0.008	0.047
threshrank	3.705	0.615	4.320
threshrankfun	0.072	0.006	0.077
tip_glom	0.932	0.005	0.926
topf	0.011	0.000	0.011
topk	0.01	0.00	0.01
topp	0.011	0.000	0.011
transformcounts	0.081	0.004	0.085
transpose-methods	0.449	0.267	0.717
tree_layout	0.482	0.004	0.464

CHECK results for phyloseq on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings