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This page was generated on 2022-06-27 11:10:03 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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CHECK results for phyloseq on nebbiolo1


To the developers/maintainers of the phyloseq package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1453/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.40.0  (landing page)
Paul J. McMurdie
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/phyloseq
git_branch: RELEASE_3_15
git_last_commit: 20bb27d
git_last_commit_date: 2022-04-26 11:10:12 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: phyloseq
Version: 1.40.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings phyloseq_1.40.0.tar.gz
StartedAt: 2022-06-26 21:14:21 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 21:18:46 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 265.8 seconds
RetCode: 0
Status:   OK  
CheckDir: phyloseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings phyloseq_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/phyloseq.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.40.0’
* 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 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
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/phyloseq.Rcheck/00check.log’
for details.



Installation output

phyloseq.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL phyloseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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] '1.40.0'
> # 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-3.15-bioc/R/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-3.15-bioc/R/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 
 57.747   1.215  58.896 

Example timings

phyloseq.Rcheck/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA2.3490.1032.453
JSD0.0000.0000.001
UniFrac-methods0.0910.0010.091
access000
assign-otu_table0.0010.0000.000
assign-phy_tree0.0330.0000.033
assign-sample_data0.1120.0000.111
assign-sample_names0.0070.0000.007
assign-tax_table0.0010.0000.001
assign-taxa_are_rows0.0020.0000.003
assign-taxa_names0.0060.0000.007
build_tax_table0.0080.0030.010
capscale-phyloseq-methods0.6090.0390.649
cca-rda-phyloseq-methods0.0000.0000.001
chunkReOrder0.0000.0000.001
data-GlobalPatterns1.4910.0791.571
data-enterotype0.960.000.96
data-esophagus0.4070.0070.416
data-soilrep1.4440.0321.476
distance0.1650.0120.179
distanceMethodList0.0010.0000.001
envHash2otu_table0.0010.0010.000
estimate_richness0.0390.0030.043
export_env_file0.0000.0000.001
export_mothur_dist0.0490.0270.077
extract-methods0.0030.0030.008
filter_taxa0.8950.0350.930
filterfun_sample0.0260.0000.025
gapstat_ord1.2310.0811.313
genefilter_sample-methods000
get.component.classes000
get_sample-methods0.0030.0000.003
get_taxa-methods0.0030.0010.004
get_taxa_unique0.2490.0110.261
get_variable0.1550.0070.164
getslots.phyloseq0.1560.0080.164
import0.0010.0010.001
import_RDP_otu0.3850.0190.405
import_biom0.8210.0570.878
import_env_file0.0000.0000.001
import_mothur0.0000.0000.001
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.8600.0010.861
import_qiime_otu_tax0.8020.2041.006
import_qiime_sample_data0.0050.0040.009
import_uparse000
import_usearch_uc0.0130.0080.021
index_reorder000
intersect_taxa000
make_network1.5140.0761.590
merge_phyloseq0.0010.0000.001
merge_phyloseq_pair-methods0.0010.0000.001
merge_samples-methods0.5870.0360.624
merge_taxa-methods0.0470.0040.052
microbio_me_qiime0.4430.0250.469
mt-methods1.2610.0161.277
nodeplotblank0.2650.0080.250
nodeplotboot0.0010.0000.002
nodeplotdefault0.0010.0000.001
nsamples-methods0.0220.0000.021
ntaxa-methods0.0000.0030.003
ordinate0.0000.0010.000
otu_table-methods000
parseTaxonomy-functions0.0000.0010.001
phy_tree-methods0.1480.0090.157
phyloseq0.0170.0040.021
phyloseq_to_deseq22.5930.0602.652
phyloseq_to_metagenomeSeq1.6120.0481.659
plot_bar1.4100.0801.491
plot_clusgap3.3140.1203.436
plot_heatmap2.2680.0802.349
plot_net2.7530.0192.687
plot_network1.3810.0441.426
plot_ordination0.5610.0160.577
plot_phyloseq-methods0.1820.0000.177
plot_richness3.5870.0523.639
plot_scree1.2330.0241.258
plot_tree0.5080.0120.508
prune_samples-methods0.3690.0000.369
prune_taxa-methods0.0400.0000.041
psmelt0.5810.0120.593
rank_names0.0220.0000.022
rarefy_even_depth0.0810.0000.081
read_tree0.0130.0000.013
read_tree_greengenes0.0090.0000.009
reconcile_categories000
refseq-methods0.1430.0060.150
rm_outlierf0.0180.0000.018
sample_data-methods0.0480.0040.053
sample_names-methods0.0000.0020.002
sample_sums0.0200.0090.029
sample_variables0.0190.0030.023
show-methods000
splat.phyloseq.objects0.0000.0000.001
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom000
tax_table-methods0.0010.0000.000
taxa_names-methods0.0180.0010.019
taxa_sums0.0210.0180.038
threshrank1.4252.0523.477
threshrankfun0.0450.0000.045
tip_glom0.5160.0200.523
topf0.0090.0030.012
topk0.0150.0010.014
topp0.0060.0040.010
transformcounts0.0750.0000.075
transpose-methods0.5101.5472.058
tree_layout0.3960.0520.426