Multiple platform build/check report for BioC 3.6 - CHECK report for phyloseq on tokay1

Package: phyloseq

Version: 1.22.3

Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.22.3.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.22.3.tar.gz

StartedAt: 2018-04-12 02:09:18 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:17:25 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 487.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: phyloseq.Rcheck

Warnings: 1

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### Running command:
###
###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.22.3.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.22.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.22.3'
* 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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/DPCoA.Rd:46: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/DPCoA.Rd:13: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/capscale-phyloseq-methods.Rd:36: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/capscale-phyloseq-methods.Rd:40: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/capscale-phyloseq-methods.Rd:65: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/cca-rda-phyloseq-methods.Rd:47: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/cca-rda-phyloseq-methods.Rd:48: missing file link 'capscale.phyloseq'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/cca-rda-phyloseq-methods.Rd:42: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/cca-rda-phyloseq-methods.Rd:57: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distance.Rd:45: missing file link 'UniFrac'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distance.Rd:46: missing file link 'UniFrac'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distanceMethodList.Rd:14: missing file link 'UniFrac'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distanceMethodList.Rd:15: missing file link 'UniFrac'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/estimate_richness.Rd:58: missing file link 'estimateR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/genefilter_sample-methods.Rd:49: missing file link 't'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/genefilter_sample-methods.Rd:66: missing file link 't'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:43: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:51: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:60: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:67: missing file link 'readDNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:74: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:163: missing file link 'biom_data'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:165: missing file link 'sample_metadata'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:167: missing file link 'observation_metadata'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_mothur.Rd:75: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:42: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:50: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:59: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:66: missing file link 'readDNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:73: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/merge_samples-methods.Rd:45: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/merge_taxa-methods.Rd:33: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:50: missing file link 'mt.minP'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:54: missing file link 'mt.minP'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:57: missing file link 'p.adjust.methods'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:63: missing file link 'mt.minP'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:67: missing file link 'mt.minP'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:89: missing file link 'mt.minP'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/ntaxa-methods.Rd:31: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/ordinate.Rd:35: missing file link 'rda'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/ordinate.Rd:38: missing file link 'capscale.phyloseq'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phy_tree-methods.Rd:8: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phy_tree-methods.Rd:33: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phy_tree-methods.Rd:25: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo-class.Rd:7: missing file link 'ape'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo-class.Rd:12: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo.Rd:12: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo.Rd:33: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq-class.Rd:12: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq-class.Rd:40: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq_to_deseq2.Rd:26: missing file link 'DESeqDataSetFromMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq_to_deseq2.Rd:60: missing file link 'DESeqDataSetFromMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_net.Rd:86: missing file link 'igraph'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_net.Rd:41: missing file link 'layout.auto'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_network.Rd:69: missing file link 'layout.fruchterman.reingold'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_ordination.Rd:58: missing file link 'scale_color_manual'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_ordination.Rd:67: missing file link 'scale_shape_manual'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_richness.Rd:36: missing file link 'scale_color_manual'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_richness.Rd:48: missing file link 'scale_shape_manual'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_richness.Rd:127: missing file link 'estimateR'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/refseq-methods.Rd:8: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/refseq-methods.Rd:33: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/refseq-methods.Rd:25: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/taxa_names-methods.Rd:34: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/tip_glom.Rd:12: missing file link 'phylo'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/tip_glom.Rd:68: missing file link 'phylo'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
* 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 : <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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plot_heatmap 5.08   0.08    5.16
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/phyloseq.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'phyloseq' ...
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/DPCoA.Rd:46: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/DPCoA.Rd:13: missing file link 'phylo'
    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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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/cca-rda-phyloseq-methods.Rd:57: missing file link 'rda'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distance.Rd:45: missing file link 'UniFrac'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distance.Rd:46: missing file link 'UniFrac'
    distanceMethodList                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distanceMethodList.Rd:14: missing file link 'UniFrac'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/distanceMethodList.Rd:15: missing file link 'UniFrac'
    envHash2otu_table                       html  
    estimate_richness                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/estimate_richness.Rd:58: missing file link 'estimateR'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/genefilter_sample-methods.Rd:49: missing file link 't'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/genefilter_sample-methods.Rd:66: missing file link 't'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:43: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:51: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:60: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:67: missing file link 'readDNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:74: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:163: missing file link 'biom_data'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:165: missing file link 'sample_metadata'
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    import_env_file                         html  
    import_mothur                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_mothur.Rd:75: missing file link 'phylo'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:42: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:50: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:59: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:66: missing file link 'readDNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_qiime.Rd:73: missing file link 'XStringSet'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/merge_samples-methods.Rd:45: missing file link 'phylo'
    merge_taxa-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/merge_taxa-methods.Rd:33: missing file link 'phylo'
    metaMDS                                 html  
    microbio_me_qiime                       html  
    mt-methods                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:50: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:54: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:57: missing file link 'p.adjust.methods'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:63: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:67: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/mt-methods.Rd:89: missing file link 'mt.minP'
    nodeplotblank                           html  
    nodeplotboot                            html  
    nodeplotdefault                         html  
    nsamples-methods                        html  
    ntaxa-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/ntaxa-methods.Rd:31: missing file link 'phylo'
    ordinate                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/ordinate.Rd:35: missing file link 'rda'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/ordinate.Rd:38: missing file link 'capscale.phyloseq'
    otu_table-class                         html  
    otu_table-methods                       html  
    parseTaxonomy-functions                 html  
    pcoa                                    html  
    phy_tree-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phy_tree-methods.Rd:8: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phy_tree-methods.Rd:33: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phy_tree-methods.Rd:25: missing file link 'phylo'
    phylo-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo-class.Rd:7: missing file link 'ape'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo-class.Rd:12: missing file link 'phylo'
    phylo                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo.Rd:12: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phylo.Rd:33: missing file link 'phylo'
    phyloseq-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq-class.Rd:12: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq-class.Rd:40: missing file link 'phylo'
    phyloseq-deprecated                     html  
    phyloseq-package                        html  
    phyloseq                                html  
    phyloseq_to_deseq2                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq_to_deseq2.Rd:26: missing file link 'DESeqDataSetFromMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/phyloseq_to_deseq2.Rd:60: missing file link 'DESeqDataSetFromMatrix'
    phyloseq_to_metagenomeSeq               html  
    plot_bar                                html  
    plot_clusgap                            html  
    plot_heatmap                            html  
    plot_net                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_net.Rd:86: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_net.Rd:41: missing file link 'layout.auto'
    plot_network                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_network.Rd:69: missing file link 'layout.fruchterman.reingold'
    plot_ordination                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_ordination.Rd:58: missing file link 'scale_color_manual'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_ordination.Rd:67: missing file link 'scale_shape_manual'
    plot_phyloseq-methods                   html  
    plot_richness                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_richness.Rd:36: missing file link 'scale_color_manual'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_richness.Rd:48: missing file link 'scale_shape_manual'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/plot_richness.Rd:127: missing file link 'estimateR'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/refseq-methods.Rd:8: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/refseq-methods.Rd:33: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/refseq-methods.Rd:25: missing file link 'phylo'
    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-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/taxa_names-methods.Rd:34: missing file link 'phylo'
    taxa_sums                               html  
    taxonomyTable-class                     html  
    threshrank                              html  
    threshrankfun                           html  
    tip_glom                                html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/tip_glom.Rd:12: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/tip_glom.Rd:68: missing file link 'phylo'
    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_1.22.3.zip
* DONE (phyloseq)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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] '1.22.3'
> # 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 â��install-tests parameter to R CMD install, or INSTALL_opts = c(â��â��install-testsâ��) argument to install.packages(). Iâ��m not sure why you wouldnâ��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-3.6-bioc/meat/phyloseq.buildbin-libdir/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-3.6-bioc/meat/phyloseq.buildbin-libdir/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
== testthat results  ===========================================================
OK: 613 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  69.89    0.84   70.82


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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] '1.22.3'
> # 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 â��install-tests parameter to R CMD install, or INSTALL_opts = c(â��â��install-testsâ��) argument to install.packages(). Iâ��m not sure why you wouldnâ��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-3.6-bioc/meat/phyloseq.buildbin-libdir/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-3.6-bioc/meat/phyloseq.buildbin-libdir/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
Processing Reference Sequences...
== testthat results  ===========================================================
OK: 613 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  67.40    1.15   68.56

name	user	system	elapsed
DPCoA	4.06	0.12	4.18
JSD	0	0	0
UniFrac-methods	0.37	0.00	0.37
access	0	0	0
assign-otu_table	0.02	0.00	0.02
assign-phy_tree	0.18	0.00	0.19
assign-sample_data	0.66	0.00	0.65
assign-sample_names	0.00	0.02	0.02
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.02	0.00	0.01
build_tax_table	0.01	0.00	0.02
capscale-phyloseq-methods	0.91	0.01	0.92
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0.01	0.00	0.02
data-GlobalPatterns	1.66	0.02	1.67
data-enterotype	2.06	0.03	2.09
data-esophagus	0.49	0.00	0.48
data-soilrep	2.20	0.01	2.22
distance	0.34	0.05	2.11
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.05	0.00	0.05
export_env_file	0	0	0
export_mothur_dist	0.06	0.02	0.08
extract-methods	0.00	0.01	0.01
filter_taxa	0.96	0.03	0.99
filterfun_sample	0.01	0.00	0.01
gapstat_ord	1.69	0.03	1.72
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.01	0.00	0.01
get_taxa-methods	0	0	0
get_taxa_unique	0.22	0.05	0.27
get_variable	0.20	0.00	0.21
getslots.phyloseq	0.24	0.00	0.23
import	0	0	0
import_RDP_otu	1.54	0.01	1.56
import_biom	0.41	0.05	0.46
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.78	0.01	0.80
import_qiime_otu_tax	0.53	0.04	0.56
import_qiime_sample_data	0.01	0.00	0.02
import_uparse	0	0	0
import_usearch_uc	0	0	0
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.69	0.00	2.69
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.31	0.09	1.41
merge_taxa-methods	0.06	0.01	0.07
microbio_me_qiime	0.94	0.02	1.05
mt-methods	2.52	0.02	2.53
nodeplotblank	0.59	0.00	0.60
nodeplotboot	0.03	0.00	0.03
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.01
ntaxa-methods	0.01	0.00	0.02
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.19	0.01	0.20
phyloseq	0.01	0.00	0.01
phyloseq_to_deseq2	2.66	0.15	2.82
phyloseq_to_metagenomeSeq	1.67	0.08	1.75
plot_bar	2.07	0.03	2.09
plot_clusgap	3.79	0.08	3.91
plot_heatmap	4.81	0.13	4.93
plot_net	3.94	0.00	3.94
plot_network	1.8	0.0	1.8
plot_ordination	0.64	0.00	0.64
plot_phyloseq-methods	0.19	0.01	0.20
plot_richness	4.33	0.05	4.38
plot_scree	2.40	0.01	2.42
plot_tree	0.66	0.02	0.64
prune_samples-methods	1.14	0.02	1.16
prune_taxa-methods	0.03	0.00	0.03
psmelt	0.83	0.03	0.86
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.14	0.00	0.14
read_tree	0.03	0.00	0.03
read_tree_greengenes	0.01	0.00	0.02
reconcile_categories	0	0	0
refseq-methods	0.24	0.00	0.23
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0.10	0.00	0.09
sample_names-methods	0.01	0.00	0.02
sample_sums	0.05	0.00	0.04
sample_variables	0.03	0.00	0.03
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.01	0.00	0.02
taxa_sums	0.03	0.02	0.04
threshrank	1.89	0.47	2.36
threshrankfun	0.06	0.00	0.06
tip_glom	0.78	0.01	0.78
topf	0.02	0.00	0.02
topk	0.01	0.00	0.01
topp	0	0	0
transformcounts	0.08	0.00	0.08
transpose-methods	0.82	0.30	1.11
tree_layout	0.56	0.00	0.56

name	user	system	elapsed
DPCoA	4.33	0.03	4.36
JSD	0	0	0
UniFrac-methods	0.40	0.01	0.42
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.19	0.00	0.19
assign-sample_data	0.46	0.02	0.47
assign-sample_names	0	0	0
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0	0	0
build_tax_table	0.02	0.00	0.02
capscale-phyloseq-methods	1.06	0.00	1.06
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	2.06	0.02	2.08
data-enterotype	1.64	0.00	1.64
data-esophagus	0.47	0.00	0.47
data-soilrep	1.89	0.00	1.89
distance	0.25	0.01	0.26
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.06	0.00	0.07
export_env_file	0	0	0
export_mothur_dist	0.05	0.02	0.06
extract-methods	0	0	0
filter_taxa	1.00	0.03	1.03
filterfun_sample	0.03	0.00	0.03
gapstat_ord	1.82	0.00	1.81
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.01	0.00	0.02
get_taxa_unique	0.19	0.03	0.22
get_variable	0.15	0.00	0.15
getslots.phyloseq	0.14	0.01	0.16
import	0	0	0
import_RDP_otu	1.06	0.04	1.09
import_biom	0.49	0.00	0.48
import_env_file	0	0	0
import_mothur	0	0	0
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.83	0.00	0.83
import_qiime_otu_tax	0.59	0.00	0.60
import_qiime_sample_data	0	0	0
import_uparse	0.01	0.00	0.02
import_usearch_uc	0	0	0
index_reorder	0	0	0
intersect_taxa	0.02	0.00	0.01
make_network	2.36	0.07	2.44
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.29	0.13	1.42
merge_taxa-methods	0.08	0.00	0.08
microbio_me_qiime	0.89	0.01	0.97
mt-methods	1.51	0.00	1.51
nodeplotblank	0.50	0.00	0.52
nodeplotboot	0.03	0.00	0.03
nodeplotdefault	0	0	0
nsamples-methods	0.04	0.00	0.03
ntaxa-methods	0.01	0.00	0.01
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.17	0.00	0.18
phyloseq	0.03	0.00	0.03
phyloseq_to_deseq2	3.10	0.08	3.17
phyloseq_to_metagenomeSeq	1.98	0.08	2.06
plot_bar	2.41	0.02	2.42
plot_clusgap	4.23	0.09	4.41
plot_heatmap	5.08	0.08	5.16
plot_net	3.63	0.01	3.64
plot_network	1.87	0.02	1.89
plot_ordination	0.61	0.05	0.65
plot_phyloseq-methods	0.19	0.00	0.19
plot_richness	4.19	0.07	4.27
plot_scree	3.07	0.02	3.09
plot_tree	0.5	0.0	0.5
prune_samples-methods	0.36	0.00	0.36
prune_taxa-methods	0.05	0.00	0.05
psmelt	0.67	0.00	0.67
rank_names	0.01	0.00	0.02
rarefy_even_depth	0.13	0.00	0.13
read_tree	0.01	0.00	0.01
read_tree_greengenes	0.02	0.00	0.02
reconcile_categories	0	0	0
refseq-methods	0.16	0.00	0.15
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0.04	0.00	0.05
sample_names-methods	0.00	0.02	0.02
sample_sums	0.02	0.01	0.03
sample_variables	0.01	0.02	0.03
show-methods	0	0	0
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0	0	0
taxa_names-methods	0.04	0.00	0.03
taxa_sums	0.01	0.01	0.03
threshrank	1.99	0.24	2.22
threshrankfun	0.06	0.00	0.06
tip_glom	0.62	0.03	0.63
topf	0	0	0
topk	0.02	0.00	0.01
topp	0	0	0
transformcounts	0.08	0.00	0.08
transpose-methods	1.02	0.30	1.31
tree_layout	0.55	0.00	0.55

CHECK report for phyloseq on tokay1

Summary

Command output

Installation output

Tests output

Example timings