Paul J. McMurdie
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/phyloseq |
| git_branch: RELEASE_3_18 |
| git_last_commit: 7320133 |
| git_last_commit_date: 2023-10-24 09:49:18 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:07 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1546/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phyloseq 1.46.0 (landing page) Paul J. McMurdie
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: phyloseq |
| Version: 1.46.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:phyloseq.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings phyloseq_1.46.0.tar.gz |
| StartedAt: 2024-03-28 03:47:33 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:52:30 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 296.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: phyloseq.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:phyloseq.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings phyloseq_1.46.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/phyloseq.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.46.0'
* 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 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 ... WARNING
checkRd: (7) import_qiime.Rd:120: Invalid URL: "http://www.qiime.org/"
* 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 ... NOTE
S3 methods shown with full name in documentation object 'cca.phyloseq':
'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 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: 1 WARNING, 3 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/phyloseq.Rcheck/00check.log'
for details.
phyloseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL phyloseq ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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)
phyloseq.Rcheck/tests/testthat-phyloseq.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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] '1.46.0'
> # 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...
F:/biocbuild/bbs-3.18-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...
F:/biocbuild/bbs-3.18-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
63.17 2.62 66.04
phyloseq.Rcheck/phyloseq-Ex.timings
| name | user | system | elapsed | |
| DPCoA | 2.65 | 0.11 | 2.75 | |
| JSD | 0 | 0 | 0 | |
| UniFrac-methods | 0.13 | 0.00 | 0.13 | |
| access | 0 | 0 | 0 | |
| assign-otu_table | 0 | 0 | 0 | |
| assign-phy_tree | 0.04 | 0.00 | 0.05 | |
| assign-sample_data | 0.10 | 0.01 | 0.11 | |
| assign-sample_names | 0 | 0 | 0 | |
| assign-tax_table | 0 | 0 | 0 | |
| assign-taxa_are_rows | 0 | 0 | 0 | |
| assign-taxa_names | 0.00 | 0.02 | 0.01 | |
| build_tax_table | 0.02 | 0.00 | 0.02 | |
| capscale-phyloseq-methods | 0.47 | 0.03 | 0.50 | |
| cca-rda-phyloseq-methods | 0 | 0 | 0 | |
| chunkReOrder | 0 | 0 | 0 | |
| data-GlobalPatterns | 1.39 | 0.01 | 1.40 | |
| data-enterotype | 1.43 | 0.02 | 1.46 | |
| data-esophagus | 0.41 | 0.01 | 0.43 | |
| data-soilrep | 0.66 | 0.07 | 0.72 | |
| distance | 0.26 | 0.04 | 0.49 | |
| distanceMethodList | 0 | 0 | 0 | |
| envHash2otu_table | 0 | 0 | 0 | |
| estimate_richness | 0.03 | 0.00 | 0.03 | |
| export_env_file | 0 | 0 | 0 | |
| export_mothur_dist | 0.11 | 0.00 | 0.11 | |
| extract-methods | 0.00 | 0.01 | 0.02 | |
| filter_taxa | 1.28 | 0.07 | 1.34 | |
| filterfun_sample | 0.02 | 0.00 | 0.02 | |
| gapstat_ord | 1.61 | 0.03 | 1.64 | |
| genefilter_sample-methods | 0 | 0 | 0 | |
| get.component.classes | 0 | 0 | 0 | |
| get_sample-methods | 0 | 0 | 0 | |
| get_taxa-methods | 0 | 0 | 0 | |
| get_taxa_unique | 0.17 | 0.00 | 0.17 | |
| get_variable | 0.12 | 0.00 | 0.12 | |
| getslots.phyloseq | 0.14 | 0.00 | 0.14 | |
| import | 0 | 0 | 0 | |
| import_RDP_otu | 0.88 | 0.03 | 0.92 | |
| import_biom | 0.14 | 0.00 | 0.15 | |
| 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 | 0.83 | 0.02 | 0.84 | |
| import_qiime_otu_tax | 0.70 | 0.06 | 0.76 | |
| import_qiime_sample_data | 0.02 | 0.00 | 0.02 | |
| import_uparse | 0 | 0 | 0 | |
| import_usearch_uc | 0.01 | 0.00 | 0.02 | |
| index_reorder | 0 | 0 | 0 | |
| intersect_taxa | 0 | 0 | 0 | |
| make_network | 1.41 | 0.06 | 1.46 | |
| merge_phyloseq | 0 | 0 | 0 | |
| merge_phyloseq_pair-methods | 0 | 0 | 0 | |
| merge_samples-methods | 0.67 | 0.05 | 0.72 | |
| merge_taxa-methods | 0.05 | 0.00 | 0.05 | |
| microbio_me_qiime | 0.62 | 0.03 | 0.73 | |
| mt-methods | 1.24 | 0.01 | 1.25 | |
| nodeplotblank | 0.31 | 0.02 | 0.33 | |
| nodeplotboot | 0 | 0 | 0 | |
| nodeplotdefault | 0 | 0 | 0 | |
| nsamples-methods | 0.02 | 0.00 | 0.01 | |
| ntaxa-methods | 0.00 | 0.02 | 0.02 | |
| ordinate | 0 | 0 | 0 | |
| otu_table-methods | 0 | 0 | 0 | |
| parseTaxonomy-functions | 0 | 0 | 0 | |
| phy_tree-methods | 0.12 | 0.00 | 0.12 | |
| phyloseq | 0.02 | 0.00 | 0.02 | |
| phyloseq_to_deseq2 | 3.64 | 0.07 | 3.72 | |
| phyloseq_to_metagenomeSeq | 2.03 | 0.08 | 2.11 | |
| plot_bar | 1.63 | 0.14 | 1.76 | |
| plot_clusgap | 2.46 | 0.08 | 2.53 | |
| plot_heatmap | 3.73 | 0.05 | 3.78 | |
| plot_net | 2.39 | 0.09 | 2.49 | |
| plot_network | 1.75 | 0.02 | 1.77 | |
| plot_ordination | 0.39 | 0.00 | 0.39 | |
| plot_phyloseq-methods | 0.22 | 0.00 | 0.22 | |
| plot_richness | 4.89 | 0.06 | 4.95 | |
| plot_scree | 1.36 | 0.00 | 1.36 | |
| plot_tree | 0.56 | 0.01 | 0.57 | |
| prune_samples-methods | 0.47 | 0.00 | 0.47 | |
| prune_taxa-methods | 0.06 | 0.02 | 0.08 | |
| psmelt | 0.54 | 0.02 | 0.55 | |
| rank_names | 0.03 | 0.00 | 0.03 | |
| rarefy_even_depth | 0.09 | 0.00 | 0.09 | |
| read_tree | 0.02 | 0.00 | 0.02 | |
| read_tree_greengenes | 0.00 | 0.00 | 0.01 | |
| reconcile_categories | 0 | 0 | 0 | |
| refseq-methods | 0.12 | 0.01 | 0.14 | |
| rm_outlierf | 0.02 | 0.00 | 0.02 | |
| sample_data-methods | 0.04 | 0.02 | 0.06 | |
| sample_names-methods | 0.00 | 0.01 | 0.02 | |
| sample_sums | 0.04 | 0.00 | 0.03 | |
| sample_variables | 0.01 | 0.00 | 0.01 | |
| 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 | 0 | 0 | |
| tax_glom | 0 | 0 | 0 | |
| tax_table-methods | 0 | 0 | 0 | |
| taxa_names-methods | 0.02 | 0.02 | 0.04 | |
| taxa_sums | 0.03 | 0.00 | 0.03 | |
| threshrank | 2.42 | 1.08 | 3.50 | |
| threshrankfun | 0.08 | 0.00 | 0.08 | |
| tip_glom | 0.65 | 0.01 | 0.67 | |
| topf | 0.02 | 0.00 | 0.01 | |
| topk | 0.02 | 0.00 | 0.02 | |
| topp | 0.01 | 0.00 | 0.01 | |
| transformcounts | 0.13 | 0.00 | 0.13 | |
| transpose-methods | 0.9 | 0.8 | 1.7 | |
| tree_layout | 0.47 | 0.01 | 0.50 | |