############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:phyloseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --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: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘phyloseq/DESCRIPTION’ ... OK * this is package ‘phyloseq’ version ‘1.50.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 : : no visible global function definition for ‘complete.cases’ nodeplotboot : : no visible binding for global variable ‘x’ nodeplotboot : : no visible binding for global variable ‘y’ nodeplotdefault : : no visible binding for global variable ‘x’ nodeplotdefault : : no visible binding for global variable ‘y’ nodeplotdefault : : 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 : : 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 re-building of vignette outputs ... OK * 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.