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CHECK report for phyloseq on tokay1

This page was generated on 2018-04-12 13:21:32 -0400 (Thu, 12 Apr 2018).

Package 1035/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phyloseq 1.22.3
Paul J. McMurdie
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/phyloseq
Branch: RELEASE_3_6
Last Commit: c695323
Last Changed Date: 2017-11-04 20:23:08 -0400 (Sat, 04 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phyloseq
Version: 1.22.3
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

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.



Installation output

phyloseq.Rcheck/00install.out


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  
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'
    cca-rda-phyloseq-methods                html  
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'
    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'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpkPAf6s/R.INSTALL19582aa2ae3/phyloseq/man/import_biom.Rd:167: missing file link 'observation_metadata'
    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

Tests output

phyloseq.Rcheck/tests_i386/testthat-phyloseq.Rout


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 –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-3.6-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 

phyloseq.Rcheck/tests_x64/testthat-phyloseq.Rout


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 –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-3.6-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 

Example timings

phyloseq.Rcheck/examples_i386/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA4.060.124.18
JSD000
UniFrac-methods0.370.000.37
access000
assign-otu_table0.020.000.02
assign-phy_tree0.180.000.19
assign-sample_data0.660.000.65
assign-sample_names0.000.020.02
assign-tax_table000
assign-taxa_are_rows000
assign-taxa_names0.020.000.01
build_tax_table0.010.000.02
capscale-phyloseq-methods0.910.010.92
cca-rda-phyloseq-methods000
chunkReOrder0.010.000.02
data-GlobalPatterns1.660.021.67
data-enterotype2.060.032.09
data-esophagus0.490.000.48
data-soilrep2.200.012.22
distance0.340.052.11
distanceMethodList000
envHash2otu_table000
estimate_richness0.050.000.05
export_env_file000
export_mothur_dist0.060.020.08
extract-methods0.000.010.01
filter_taxa0.960.030.99
filterfun_sample0.010.000.01
gapstat_ord1.690.031.72
genefilter_sample-methods000
get.component.classes000
get_sample-methods0.010.000.01
get_taxa-methods000
get_taxa_unique0.220.050.27
get_variable0.200.000.21
getslots.phyloseq0.240.000.23
import000
import_RDP_otu1.540.011.56
import_biom0.410.050.46
import_env_file000
import_mothur000
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.780.010.80
import_qiime_otu_tax0.530.040.56
import_qiime_sample_data0.010.000.02
import_uparse000
import_usearch_uc000
index_reorder000
intersect_taxa000
make_network2.690.002.69
merge_phyloseq000
merge_phyloseq_pair-methods000
merge_samples-methods1.310.091.41
merge_taxa-methods0.060.010.07
microbio_me_qiime0.940.021.05
mt-methods2.520.022.53
nodeplotblank0.590.000.60
nodeplotboot0.030.000.03
nodeplotdefault000
nsamples-methods0.020.000.01
ntaxa-methods0.010.000.02
ordinate000
otu_table-methods000
parseTaxonomy-functions000
phy_tree-methods0.190.010.20
phyloseq0.010.000.01
phyloseq_to_deseq22.660.152.82
phyloseq_to_metagenomeSeq1.670.081.75
plot_bar2.070.032.09
plot_clusgap3.790.083.91
plot_heatmap4.810.134.93
plot_net3.940.003.94
plot_network1.80.01.8
plot_ordination0.640.000.64
plot_phyloseq-methods0.190.010.20
plot_richness4.330.054.38
plot_scree2.400.012.42
plot_tree0.660.020.64
prune_samples-methods1.140.021.16
prune_taxa-methods0.030.000.03
psmelt0.830.030.86
rank_names0.030.000.03
rarefy_even_depth0.140.000.14
read_tree0.030.000.03
read_tree_greengenes0.010.000.02
reconcile_categories000
refseq-methods0.240.000.23
rm_outlierf0.030.000.03
sample_data-methods0.100.000.09
sample_names-methods0.010.000.02
sample_sums0.050.000.04
sample_variables0.030.000.03
show-methods000
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom000
tax_table-methods000
taxa_names-methods0.010.000.02
taxa_sums0.030.020.04
threshrank1.890.472.36
threshrankfun0.060.000.06
tip_glom0.780.010.78
topf0.020.000.02
topk0.010.000.01
topp000
transformcounts0.080.000.08
transpose-methods0.820.301.11
tree_layout0.560.000.56

phyloseq.Rcheck/examples_x64/phyloseq-Ex.timings

nameusersystemelapsed
DPCoA4.330.034.36
JSD000
UniFrac-methods0.400.010.42
access000
assign-otu_table000
assign-phy_tree0.190.000.19
assign-sample_data0.460.020.47
assign-sample_names000
assign-tax_table000
assign-taxa_are_rows000
assign-taxa_names000
build_tax_table0.020.000.02
capscale-phyloseq-methods1.060.001.06
cca-rda-phyloseq-methods000
chunkReOrder000
data-GlobalPatterns2.060.022.08
data-enterotype1.640.001.64
data-esophagus0.470.000.47
data-soilrep1.890.001.89
distance0.250.010.26
distanceMethodList000
envHash2otu_table000
estimate_richness0.060.000.07
export_env_file000
export_mothur_dist0.050.020.06
extract-methods000
filter_taxa1.000.031.03
filterfun_sample0.030.000.03
gapstat_ord1.820.001.81
genefilter_sample-methods000
get.component.classes000
get_sample-methods000
get_taxa-methods0.010.000.02
get_taxa_unique0.190.030.22
get_variable0.150.000.15
getslots.phyloseq0.140.010.16
import000
import_RDP_otu1.060.041.09
import_biom0.490.000.48
import_env_file000
import_mothur000
import_mothur_dist000
import_pyrotagger_tab000
import_qiime0.830.000.83
import_qiime_otu_tax0.590.000.60
import_qiime_sample_data000
import_uparse0.010.000.02
import_usearch_uc000
index_reorder000
intersect_taxa0.020.000.01
make_network2.360.072.44
merge_phyloseq000
merge_phyloseq_pair-methods000
merge_samples-methods1.290.131.42
merge_taxa-methods0.080.000.08
microbio_me_qiime0.890.010.97
mt-methods1.510.001.51
nodeplotblank0.500.000.52
nodeplotboot0.030.000.03
nodeplotdefault000
nsamples-methods0.040.000.03
ntaxa-methods0.010.000.01
ordinate000
otu_table-methods000
parseTaxonomy-functions000
phy_tree-methods0.170.000.18
phyloseq0.030.000.03
phyloseq_to_deseq23.100.083.17
phyloseq_to_metagenomeSeq1.980.082.06
plot_bar2.410.022.42
plot_clusgap4.230.094.41
plot_heatmap5.080.085.16
plot_net3.630.013.64
plot_network1.870.021.89
plot_ordination0.610.050.65
plot_phyloseq-methods0.190.000.19
plot_richness4.190.074.27
plot_scree3.070.023.09
plot_tree0.50.00.5
prune_samples-methods0.360.000.36
prune_taxa-methods0.050.000.05
psmelt0.670.000.67
rank_names0.010.000.02
rarefy_even_depth0.130.000.13
read_tree0.010.000.01
read_tree_greengenes0.020.000.02
reconcile_categories000
refseq-methods0.160.000.15
rm_outlierf0.030.000.03
sample_data-methods0.040.000.05
sample_names-methods0.000.020.02
sample_sums0.020.010.03
sample_variables0.010.020.03
show-methods000
splat.phyloseq.objects000
subset_ord_plot000
subset_samples-methods000
subset_taxa-methods000
tax_glom000
tax_table-methods000
taxa_names-methods0.040.000.03
taxa_sums0.010.010.03
threshrank1.990.242.22
threshrankfun0.060.000.06
tip_glom0.620.030.63
topf000
topk0.020.000.01
topp000
transformcounts0.080.000.08
transpose-methods1.020.301.31
tree_layout0.550.000.55