Paul J. McMurdie
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/phyloseq |
| Branch: RELEASE_3_9 |
| Last Commit: a86ed1e |
| Last Changed Date: 2019-05-02 11:53:34 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:26:08 -0400 (Wed, 16 Oct 2019).
| Package 1209/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phyloseq 1.28.0 Paul J. McMurdie
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: phyloseq |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phyloseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings phyloseq_1.28.0.tar.gz |
| StartedAt: 2019-10-16 05:58:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:08:08 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 548.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: phyloseq.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phyloseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings phyloseq_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'phyloseq/DESCRIPTION' ... OK * this is package 'phyloseq' version '1.28.0' * 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 ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/DPCoA.Rd:46: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/DPCoA.Rd:13: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/capscale-phyloseq-methods.Rd:36: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/capscale-phyloseq-methods.Rd:40: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/capscale-phyloseq-methods.Rd:65: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/cca-rda-phyloseq-methods.Rd:47: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/cca-rda-phyloseq-methods.Rd:48: file link 'capscale.phyloseq' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/cca-rda-phyloseq-methods.Rd:42: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/cca-rda-phyloseq-methods.Rd:57: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/distance.Rd:46: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/distance.Rd:47: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/distanceMethodList.Rd:14: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/distanceMethodList.Rd:15: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/estimate_richness.Rd:58: file link 'estimateR' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/genefilter_sample-methods.Rd:49: file link 't' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/genefilter_sample-methods.Rd:66: file link 't' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:43: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:51: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:60: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:67: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:74: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:163: file link 'biom_data' in package 'biomformat' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:165: file link 'sample_metadata' in package 'biomformat' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:167: file link 'observation_metadata' in package 'biomformat' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_mothur.Rd:76: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_qiime.Rd:42: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_qiime.Rd:50: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_qiime.Rd:59: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_qiime.Rd:66: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_qiime.Rd:73: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/merge_samples-methods.Rd:45: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/merge_taxa-methods.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:50: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:54: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:57: file link 'p.adjust.methods' in package 'stats' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:63: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:67: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:89: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/ntaxa-methods.Rd:31: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/ordinate.Rd:36: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/ordinate.Rd:39: file link 'capscale.phyloseq' in package 'phyloseq' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phy_tree-methods.Rd:8: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phy_tree-methods.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phy_tree-methods.Rd:25: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phylo-class.Rd:7: file link 'ape' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phylo-class.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phylo.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phylo.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phyloseq-class.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phyloseq-class.Rd:40: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phyloseq_to_deseq2.Rd:26: file link 'DESeqDataSetFromMatrix' in package 'DESeq2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phyloseq_to_deseq2.Rd:60: file link 'DESeqDataSetFromMatrix' in package 'DESeq2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_net.Rd:86: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_net.Rd:41: file link 'layout.auto' in package 'igraph' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_network.Rd:69: file link 'layout.fruchterman.reingold' in package 'igraph' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_ordination.Rd:58: file link 'scale_color_manual' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_ordination.Rd:67: file link 'scale_shape_manual' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_richness.Rd:36: file link 'scale_color_manual' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_richness.Rd:48: file link 'scale_shape_manual' in package 'ggplot2' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_richness.Rd:127: file link 'estimateR' in package 'vegan' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/refseq-methods.Rd:8: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/refseq-methods.Rd:33: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/refseq-methods.Rd:25: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/taxa_names-methods.Rd:34: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/tip_glom.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/tip_glom.Rd:68: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck/00install.out' for details. * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 :: 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 ... 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 ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed plot_heatmap 7.22 0.13 7.36 plot_net 4.89 0.14 5.00 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed plot_heatmap 7.48 0.05 7.53 plot_net 5.05 0.06 5.08 plot_clusgap 4.05 0.03 5.22 plot_bar 3.61 0.05 5.28 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat-phyloseq.R' OK ** running tests for arch 'x64' ... 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, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/phyloseq.Rcheck/00check.log' for details.
phyloseq.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/phyloseq_1.28.0.tar.gz && rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL phyloseq_1.28.0.zip && rm phyloseq_1.28.0.tar.gz phyloseq_1.28.0.zip
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install for i386
* installing *source* package 'phyloseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'phyloseq'
finding HTML links ... done
DPCoA html
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JSD html
UniFrac-methods html
finding level-2 HTML links ... done
access html
assign-otu_table html
assign-phy_tree html
assign-sample_data html
assign-sample_names html
assign-tax_table html
assign-taxa_are_rows html
assign-taxa_names html
build_tax_table html
capscale-phyloseq-methods html
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cca-rda-phyloseq-methods html
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chunkReOrder html
data-GlobalPatterns html
data-enterotype html
data-esophagus html
data-soilrep html
decorana html
dist-class html
distance html
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distanceMethodList html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/distanceMethodList.Rd:14: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/distanceMethodList.Rd:15: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
envHash2otu_table html
estimate_richness html
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export_env_file html
export_mothur_dist html
extract-methods html
filter_taxa html
filterfun_sample html
fix_phylo html
gapstat_ord html
genefilter_sample-methods html
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Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/genefilter_sample-methods.Rd:66: file link 't' in package 'phyloseq' does not exist and so has been treated as a topic
get.component.classes html
get_sample-methods html
get_taxa-methods html
get_taxa_unique html
get_variable html
getslots.phyloseq html
import html
import_RDP_cluster html
import_RDP_otu html
import_biom html
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Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:51: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:60: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:67: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:74: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:163: file link 'biom_data' in package 'biomformat' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:165: file link 'sample_metadata' in package 'biomformat' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/import_biom.Rd:167: file link 'observation_metadata' in package 'biomformat' does not exist and so has been treated as a topic
import_env_file html
import_mothur html
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import_mothur_constaxonomy html
import_mothur_dist html
import_mothur_groups html
import_mothur_otu_table html
import_mothur_otulist html
import_mothur_shared html
import_pyrotagger_tab html
import_qiime html
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import_qiime_otu_tax html
import_qiime_sample_data html
import_uparse html
import_usearch_uc html
index_reorder html
intersect_taxa html
make_network html
merge_phyloseq html
merge_phyloseq_pair-methods html
merge_samples-methods html
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merge_taxa-methods html
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metaMDS html
microbio_me_qiime html
mt-methods html
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Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:57: file link 'p.adjust.methods' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:63: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:67: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/mt-methods.Rd:89: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
nodeplotblank html
nodeplotboot html
nodeplotdefault html
nsamples-methods html
ntaxa-methods html
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ordinate html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/ordinate.Rd:36: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/ordinate.Rd:39: file link 'capscale.phyloseq' in package 'phyloseq' does not exist and so has been treated as a topic
otu_table-class html
otu_table-methods html
parseTaxonomy-functions html
pcoa html
phy_tree-methods html
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Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phy_tree-methods.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
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phylo-class html
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phylo html
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Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/phylo.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
phyloseq-class html
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phyloseq-deprecated html
phyloseq-package html
phyloseq html
phyloseq_to_deseq2 html
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phyloseq_to_metagenomeSeq html
plot_bar html
plot_clusgap html
plot_heatmap html
plot_net html
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Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/plot_net.Rd:41: file link 'layout.auto' in package 'igraph' does not exist and so has been treated as a topic
plot_network html
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plot_ordination html
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plot_phyloseq-methods html
plot_richness html
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plot_scree html
plot_tree html
prune_samples-methods html
prune_taxa-methods html
psmelt html
rank_names html
rarefy_even_depth html
read_tree html
read_tree_greengenes html
reconcile_categories html
refseq-methods html
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rm_outlierf html
sample_data-class html
sample_data-methods html
sample_names-methods html
sample_sums html
sample_variables html
show-methods html
show_mothur_cutoffs html
splat.phyloseq.objects html
subset_ord_plot html
subset_samples-methods html
subset_taxa-methods html
tax_glom html
tax_table-methods html
taxa_are_rows-methods html
taxa_names-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/taxa_names-methods.Rd:34: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
taxa_sums html
taxonomyTable-class html
threshrank html
threshrankfun html
tip_glom html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/tip_glom.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpS2U6UL/R.INSTALL13e83bf469a8/phyloseq/man/tip_glom.Rd:68: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
topf html
topk html
topp html
transformcounts html
transpose-methods html
tree_layout html
** 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
install for x64
* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.28.0.zip
* DONE (phyloseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'phyloseq' successfully unpacked and MD5 sums checked
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phyloseq.Rcheck/tests_i386/testthat-phyloseq.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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] '1.28.0'
> # 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...
C:/Users/biocbuild/bbs-3.9-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...
C:/Users/biocbuild/bbs-3.9-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
== testthat results ===========================================================
[ OK: 604 | SKIPPED: 0 | WARNINGS: 49 | FAILED: 0 ]
>
> proc.time()
user system elapsed
71.10 1.57 73.26
|
phyloseq.Rcheck/tests_x64/testthat-phyloseq.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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] '1.28.0'
> # 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...
C:/Users/biocbuild/bbs-3.9-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...
C:/Users/biocbuild/bbs-3.9-bioc/R/library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
== testthat results ===========================================================
[ OK: 604 | SKIPPED: 0 | WARNINGS: 49 | FAILED: 0 ]
>
> proc.time()
user system elapsed
104.34 1.39 105.71
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phyloseq.Rcheck/examples_i386/phyloseq-Ex.timings
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phyloseq.Rcheck/examples_x64/phyloseq-Ex.timings
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