Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1389/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
phyloseq 1.36.0 (landing page) Paul J. McMurdie
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: phyloseq |
Version: 1.36.0 |
Command: /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 |
StartedAt: 2021-10-14 22:19:32 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:25:46 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 373.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: phyloseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /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 ### ############################################################################## ############################################################################## * 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.
phyloseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phyloseq ### ############################################################################## ############################################################################## * 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)
phyloseq.Rcheck/tests/testthat-phyloseq.Rout
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
phyloseq.Rcheck/phyloseq-Ex.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 | |