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BUILD BIN report for phyloseq on tokay2

This page was generated on 2018-10-17 08:36:02 -0400 (Wed, 17 Oct 2018).

Package 1092/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.24.2
Paul J. McMurdie
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/phyloseq
Branch: RELEASE_3_7
Last Commit: 829992f
Last Changed Date: 2018-07-15 15:50:17 -0400 (Sun, 15 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phyloseq
Version: 1.24.2
Command: rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.24.2.tar.gz
StartedAt: 2018-10-17 06:47:32 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 06:48:19 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 47.5 seconds
RetCode: 0
Status:  OK  
PackageFile: phyloseq_1.24.2.zip
PackageFileSize: 4.362 MiB

Command output

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###
### Running command:
###
###   rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.24.2.tar.gz
###
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install for i386

* installing *source* package 'phyloseq' ...
** 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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/DPCoA.Rd:13: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/capscale-phyloseq-methods.Rd:65: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
    cca-rda-phyloseq-methods                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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
    chunkReOrder                            html  
    data-GlobalPatterns                     html  
    data-enterotype                         html  
    data-esophagus                          html  
    data-soilrep                            html  
    decorana                                html  
    dist-class                              html  
    distance                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/distance.Rd:45: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/distance.Rd:46: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
    distanceMethodList                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/estimate_richness.Rd:58: file link 'estimateR' in package 'vegan' does not exist and so has been treated as a topic
    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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_mothur.Rd:75: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_qiime.Rd:73: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/merge_samples-methods.Rd:45: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    merge_taxa-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/merge_taxa-methods.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    metaMDS                                 html  
    microbio_me_qiime                       html  
    mt-methods                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/ntaxa-methods.Rd:31: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    ordinate                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/ordinate.Rd:35: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/ordinate.Rd:38: 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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phy_tree-methods.Rd:25: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    phylo-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phylo-class.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    phylo                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phyloseq-class.Rd:40: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    phyloseq-deprecated                     html  
    phyloseq-package                        html  
    phyloseq                                html  
    phyloseq_to_deseq2                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phyloseq_to_deseq2.Rd:60: file link 'DESeqDataSetFromMatrix' in package 'DESeq2' does not exist and so has been treated as a topic
    phyloseq_to_metagenomeSeq               html  
    plot_bar                                html  
    plot_clusgap                            html  
    plot_heatmap                            html  
    plot_net                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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
    plot_ordination                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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
    plot_phyloseq-methods                   html  
    plot_richness                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_richness.Rd:127: file link 'estimateR' in package 'vegan' does not exist and so has been treated as a topic
    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  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/refseq-methods.Rd:25: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/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
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.24.2.zip
* DONE (phyloseq)
In R CMD INSTALL
In R CMD INSTALL