############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/phyloseq_1.38.0.tar.gz && rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL phyloseq_1.38.0.zip && rm phyloseq_1.38.0.tar.gz phyloseq_1.38.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1738k 100 1738k 0 0 2562k 0 --:--:-- --:--:-- --:--:-- 2567k 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 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 cca-rda-phyloseq-methods html chunkReOrder html data-GlobalPatterns html data-enterotype html data-esophagus html data-soilrep html decorana html dist-class html distance html distanceMethodList html envHash2otu_table html estimate_richness html 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 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 import_env_file html import_mothur html 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 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 merge_taxa-methods html metaMDS html microbio_me_qiime html mt-methods html nodeplotblank html nodeplotboot html nodeplotdefault html nsamples-methods html ntaxa-methods html ordinate html otu_table-class html otu_table-methods html parseTaxonomy-functions html pcoa html phy_tree-methods html phylo-class html phylo html phyloseq-class html phyloseq-deprecated html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/phyloseq.buildbin-libdir/00LOCK-phyloseq/00new/phyloseq/help/taxTab.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/phyloseq.buildbin-libdir/00LOCK-phyloseq/00new/phyloseq/help/speciesAreRows.html phyloseq-package html phyloseq html phyloseq_to_deseq2 html phyloseq_to_metagenomeSeq html plot_bar html plot_clusgap html plot_heatmap html plot_net html plot_network html plot_ordination html plot_phyloseq-methods html plot_richness html 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 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 taxa_sums html taxonomyTable-class html threshrank html threshrankfun html tip_glom html 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_1.38.0.zip * DONE (phyloseq) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'phyloseq' successfully unpacked and MD5 sums checked