Multiple platform build/check report for BioC 3.13 - CHECK results for phyloseq on machv2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phyloseq_1.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/phyloseq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.36.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  .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 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
threshrank 2.884   2.88   5.935
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phyloseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
   ‘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
* DONE (phyloseq)

Tests output


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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] '1.36.0'
> # 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...
 /Library/Frameworks/R.framework/Versions/4.1/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/4.1/Resources/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 
 81.581   2.971  84.690

Example timings

name	user	system	elapsed
DPCoA	3.466	0.116	3.593
JSD	0.000	0.001	0.001
UniFrac-methods	0.113	0.003	0.117
access	0	0	0
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.044	0.002	0.046
assign-sample_data	0.224	0.027	0.251
assign-sample_names	0.012	0.002	0.013
assign-tax_table	0.001	0.000	0.000
assign-taxa_are_rows	0.002	0.001	0.004
assign-taxa_names	0.009	0.003	0.011
build_tax_table	0.016	0.001	0.018
capscale-phyloseq-methods	0.865	0.029	0.895
cca-rda-phyloseq-methods	0.001	0.000	0.000
chunkReOrder	0.000	0.001	0.001
data-GlobalPatterns	1.334	0.066	1.402
data-enterotype	1.735	0.064	1.801
data-esophagus	0.783	0.005	0.790
data-soilrep	1.848	0.190	2.039
distance	0.273	0.034	0.313
distanceMethodList	0.001	0.001	0.001
envHash2otu_table	0	0	0
estimate_richness	0.037	0.004	0.041
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.091	0.056	0.147
extract-methods	0.011	0.003	0.013
filter_taxa	1.295	0.051	1.347
filterfun_sample	0.028	0.001	0.029
gapstat_ord	1.680	0.035	1.717
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0	0	0
get_sample-methods	0.004	0.003	0.006
get_taxa-methods	0.004	0.002	0.006
get_taxa_unique	0.245	0.015	0.260
get_variable	0.198	0.003	0.200
getslots.phyloseq	0.265	0.003	0.268
import	0	0	0
import_RDP_otu	0.697	0.018	0.715
import_biom	0.235	0.011	0.248
import_env_file	0	0	0
import_mothur	0.000	0.001	0.000
import_mothur_dist	0.000	0.000	0.001
import_pyrotagger_tab	0	0	0
import_qiime	0.970	0.009	0.982
import_qiime_otu_tax	0.825	0.121	0.947
import_qiime_sample_data	0.014	0.003	0.017
import_uparse	0.000	0.001	0.000
import_usearch_uc	0.021	0.012	0.034
index_reorder	0	0	0
intersect_taxa	0.000	0.000	0.001
make_network	2.685	0.018	2.705
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.762	0.047	0.810
merge_taxa-methods	0.072	0.001	0.073
microbio_me_qiime	0.633	0.015	0.651
mt-methods	1.537	0.013	1.550
nodeplotblank	0.322	0.004	0.327
nodeplotboot	0.002	0.000	0.002
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.021	0.001	0.021
ntaxa-methods	0.002	0.001	0.003
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0.002	0.000	0.002
phy_tree-methods	0.162	0.002	0.164
phyloseq	0.021	0.001	0.022
phyloseq_to_deseq2	4.609	0.098	4.711
phyloseq_to_metagenomeSeq	1.078	0.060	1.140
plot_bar	2.911	0.110	3.025
plot_clusgap	3.764	0.084	3.861
plot_heatmap	3.304	0.088	3.399
plot_net	3.433	0.059	3.502
plot_network	2.239	0.028	2.270
plot_ordination	0.741	0.017	0.758
plot_phyloseq-methods	0.251	0.003	0.254
plot_richness	3.628	0.285	3.919
plot_scree	1.781	0.046	1.833
plot_tree	0.632	0.033	0.668
prune_samples-methods	0.507	0.022	0.531
prune_taxa-methods	0.052	0.002	0.054
psmelt	0.812	0.065	0.878
rank_names	0.023	0.001	0.024
rarefy_even_depth	0.107	0.002	0.109
read_tree	0.025	0.001	0.028
read_tree_greengenes	0.013	0.001	0.015
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.224	0.003	0.227
rm_outlierf	0.021	0.002	0.023
sample_data-methods	0.072	0.003	0.074
sample_names-methods	0.003	0.002	0.004
sample_sums	0.037	0.014	0.050
sample_variables	0.029	0.002	0.031
show-methods	0.000	0.001	0.000
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0	0	0
subset_samples-methods	0.000	0.001	0.000
subset_taxa-methods	0	0	0
tax_glom	0.000	0.001	0.001
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.034	0.004	0.038
taxa_sums	0.038	0.012	0.048
threshrank	2.884	2.880	5.935
threshrankfun	0.067	0.005	0.073
tip_glom	0.654	0.003	0.658
topf	0.015	0.001	0.017
topk	0.015	0.000	0.015
topp	0.011	0.001	0.012
transformcounts	0.129	0.006	0.134
transpose-methods	0.979	1.580	2.649
tree_layout	0.499	0.013	0.514

CHECK results for phyloseq on machv2

Summary

Command output

Installation output

Tests output

Example timings