Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1548/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.50.0  (landing page)
Paul J. McMurdie
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/phyloseq
git_branch: RELEASE_3_20
git_last_commit: 8724974
git_last_commit_date: 2024-10-29 09:40:05 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for phyloseq on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: phyloseq
Version: 1.50.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings phyloseq_1.50.0.tar.gz
StartedAt: 2024-11-20 11:00:39 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:06:07 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 327.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: phyloseq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings phyloseq_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/phyloseq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.50.0’
* 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 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 ... 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 ... OK
* 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/phyloseq.Rcheck/00check.log’
for details.


Installation output

phyloseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL phyloseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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

phyloseq.Rcheck/tests/testthat-phyloseq.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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] '1.50.0'
> # 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/R/R-4.4.1/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/R/R-4.4.1/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
[ FAIL 0 | WARN 51 | SKIP 0 | PASS 604 ]

[ FAIL 0 | WARN 51 | SKIP 0 | PASS 604 ]
> 
> proc.time()
   user  system elapsed 
 73.369   1.135  74.570 

Example timings

phyloseq.Rcheck/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA2.6670.1362.588
JSD0.0010.0000.000
UniFrac-methods0.1120.0000.112
access0.0010.0000.001
assign-otu_table000
assign-phy_tree0.0400.0000.041
assign-sample_data0.1110.0040.115
assign-sample_names0.0080.0000.008
assign-tax_table000
assign-taxa_are_rows0.0020.0000.002
assign-taxa_names0.0050.0000.006
build_tax_table0.0120.0000.011
capscale-phyloseq-methods0.6580.0120.672
cca-rda-phyloseq-methods000
chunkReOrder000
data-GlobalPatterns1.6550.0721.730
data-enterotype0.9620.0040.968
data-esophagus0.5770.0240.604
data-soilrep1.5950.0201.619
distance0.2040.0080.218
distanceMethodList0.0000.0000.001
envHash2otu_table0.0010.0000.000
estimate_richness0.0270.0000.026
export_env_file000
export_mothur_dist0.0400.0080.048
extract-methods0.0080.0000.007
filter_taxa1.4350.0121.450
filterfun_sample0.0180.0000.018
gapstat_ord1.6260.0441.673
genefilter_sample-methods000
get.component.classes000
get_sample-methods0.0000.0030.003
get_taxa-methods0.0030.0010.003
get_taxa_unique0.2230.0040.227
get_variable0.1650.0000.166
getslots.phyloseq0.1660.0040.171
import000
import_RDP_otu0.5900.0030.645
import_biom0.1370.0050.143
import_env_file000
import_mothur0.0010.0000.000
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.9530.0350.993
import_qiime_otu_tax0.8700.0110.884
import_qiime_sample_data0.010.000.01
import_uparse000
import_usearch_uc0.0150.0000.016
index_reorder000
intersect_taxa000
make_network1.8410.0391.886
merge_phyloseq0.0000.0000.001
merge_phyloseq_pair-methods000
merge_samples-methods0.7160.0040.721
merge_taxa-methods0.0620.0000.062
microbio_me_qiime0.6000.0140.616
mt-methods1.6660.0161.691
nodeplotblank0.4290.0170.446
nodeplotboot0.0010.0000.001
nodeplotdefault0.0000.0000.001
nsamples-methods0.0250.0000.025
ntaxa-methods0.0030.0000.003
ordinate000
otu_table-methods000
parseTaxonomy-functions0.0020.0000.001
phy_tree-methods0.1550.0030.159
phyloseq0.0260.0000.025
phyloseq_to_deseq24.7550.1044.868
phyloseq_to_metagenomeSeq2.1680.0762.297
plot_bar1.8600.0281.893
plot_clusgap4.0130.0323.914
plot_heatmap3.3230.0403.371
plot_net3.3590.0123.372
plot_network1.4440.0321.479
plot_ordination0.5580.0200.578
plot_phyloseq-methods0.2360.0040.241
plot_richness3.8510.0243.931
plot_scree1.8800.0001.884
plot_tree0.6070.0080.616
prune_samples-methods0.4020.0040.407
prune_taxa-methods0.0460.0040.050
psmelt0.6970.0040.702
rank_names0.020.000.02
rarefy_even_depth0.0990.0000.098
read_tree0.0150.0000.015
read_tree_greengenes0.010.000.01
reconcile_categories000
refseq-methods0.1500.0040.154
rm_outlierf0.0200.0000.019
sample_data-methods0.0530.0000.052
sample_names-methods0.0020.0000.002
sample_sums0.0200.0060.026
sample_variables0.0180.0010.020
show-methods0.0000.0000.001
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom000
tax_table-methods000
taxa_names-methods0.0210.0030.024
taxa_sums0.0280.0000.028
threshrank3.3980.2993.705
threshrankfun0.0560.0000.057
tip_glom0.7510.0000.751
topf0.0120.0000.013
topk0.0120.0000.012
topp0.0120.0000.013
transformcounts0.1040.0000.104
transpose-methods0.3870.2120.599
tree_layout0.6660.0320.699