BioC 3.3: CHECK report for phyloseq on moscato2

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### Running command:
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###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.16.2.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.16.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/phyloseq.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.16.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'phyloseq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
':::' calls which should be '::':
  'ape:::node_depth_edgelength' 'ape:::node_height'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .C(ape:::node_depth_edgelength, ..., PACKAGE = "ape")
  .C(ape:::node_height, ..., PACKAGE = "ape")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_clusgap  6.24   0.05    6.38
plot_net      5.94   0.00    6.59
plot_heatmap  5.58   0.05    5.82
plot_richness 5.53   0.03    5.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_heatmap  7.16   0.03    7.19
plot_clusgap  6.59   0.12    6.74
plot_net      6.52   0.03    6.55
plot_richness 5.85   0.11    6.13
DPCoA         4.85   0.05    5.15
* 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.3-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
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.16.2.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	4.20	0.02	4.41
JSD	0	0	0
UniFrac-methods	0.11	0.01	0.12
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.03	0.00	0.03
assign-sample_data	0.56	0.00	0.56
assign-sample_names	0.01	0.00	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0.02	0.00	0.02
assign-taxa_names	0	0	0
build_tax_table	0.02	0.00	0.02
capscale-phyloseq-methods	0.85	0.01	0.87
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.97	0.00	1.96
data-enterotype	2.43	0.03	2.47
data-esophagus	0.86	0.00	0.86
data-soilrep	2.51	0.02	2.53
distance	0.31	0.05	2.08
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.02	0.01	0.03
export_env_file	0	0	0
export_mothur_dist	0.06	0.02	0.07
extract-methods	0	0	0
filter_taxa	1.25	0.05	1.29
filterfun_sample	0.01	0.00	0.02
gapstat_ord	2.53	0.01	2.57
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0.00	0.02	0.02
get_taxa-methods	0	0	0
get_taxa_unique	0.30	0.03	0.32
get_variable	0.48	0.01	0.50
getslots.phyloseq	0.25	0.00	0.25
import	0	0	0
import_RDP_otu	2.2	0.0	2.2
import_biom	0.23	0.00	0.24
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	0.74	0.00	0.73
import_qiime_otu_tax	0.64	0.05	0.69
import_qiime_sample_data	0.03	0.00	0.03
import_uparse	0	0	0
import_usearch_uc	0.03	0.00	0.03
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	4.30	0.05	4.35
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.69	0.03	1.72
merge_taxa-methods	0.06	0.00	0.06
microbio_me_qiime	0.83	0.00	1.43
mt-methods	2.99	0.00	3.00
nodeplotblank	0.27	0.00	0.27
nodeplotboot	0.01	0.00	0.01
nodeplotdefault	0	0	0
nsamples-methods	0.02	0.00	0.02
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.24	0.00	0.24
phyloseq	0.01	0.00	0.01
phyloseq_to_deseq2	2.56	0.00	2.56
phyloseq_to_metagenomeSeq	1.95	0.06	2.03
plot_bar	3.33	0.03	3.35
plot_clusgap	6.24	0.05	6.38
plot_heatmap	5.58	0.05	5.82
plot_net	5.94	0.00	6.59
plot_network	3.33	0.00	3.44
plot_ordination	0.96	0.02	0.98
plot_phyloseq-methods	0.32	0.00	0.31
plot_richness	5.53	0.03	5.57
plot_scree	2.61	0.01	2.62
plot_tree	1	0	1
prune_samples-methods	1.23	0.00	1.23
prune_taxa-methods	0.05	0.00	0.05
psmelt	1	0	1
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.09	0.00	0.09
read_tree	0.14	0.00	0.14
read_tree_greengenes	0.08	0.00	0.08
reconcile_categories	0	0	0
refseq-methods	0.33	0.00	0.33
rm_outlierf	0.01	0.00	0.02
sample_data-methods	0.04	0.00	0.05
sample_names-methods	0.02	0.00	0.01
sample_sums	0.03	0.00	0.03
sample_variables	0.03	0.00	0.04
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	0.03	0.00	0.03
taxa_sums	0.03	0.02	0.05
threshrank	3.17	0.45	3.62
threshrankfun	0.04	0.02	0.06
tip_glom	0.94	0.00	0.94
topf	0.02	0.00	0.01
topk	0.01	0.00	0.02
topp	0.02	0.00	0.01
transformcounts	0.11	0.00	0.11
transpose-methods	1.73	0.26	2.00
tree_layout	0.78	0.02	0.81

name	user	system	elapsed
DPCoA	4.85	0.05	5.15
JSD	0	0	0
UniFrac-methods	0.23	0.00	0.23
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.07	0.01	0.08
assign-sample_data	1.00	0.03	1.03
assign-sample_names	0.00	0.02	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.00	0.01	0.01
build_tax_table	0.00	0.02	0.01
capscale-phyloseq-methods	1.04	0.01	1.07
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.70	0.02	1.71
data-enterotype	3.25	0.00	3.24
data-esophagus	1.17	0.00	1.17
data-soilrep	2.37	0.05	2.42
distance	0.22	0.03	0.25
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.03	0.00	0.03
export_env_file	0	0	0
export_mothur_dist	0.08	0.02	0.09
extract-methods	0.00	0.01	0.02
filter_taxa	2.13	0.03	2.17
filterfun_sample	0.03	0.00	0.03
gapstat_ord	2.69	0.11	2.79
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.00	0.02	0.02
get_taxa_unique	0.22	0.01	0.23
get_variable	0.18	0.00	0.19
getslots.phyloseq	0.20	0.00	0.21
import	0	0	0
import_RDP_otu	1.73	0.02	1.75
import_biom	0.22	0.00	0.22
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	0.92	0.00	0.92
import_qiime_otu_tax	0.78	0.00	0.78
import_qiime_sample_data	0.02	0.01	0.04
import_uparse	0	0	0
import_usearch_uc	0.01	0.02	0.03
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	4.20	0.01	4.21
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	1.81	0.02	1.82
merge_taxa-methods	0.06	0.00	0.07
microbio_me_qiime	0.78	0.00	0.96
mt-methods	2.33	0.00	2.33
nodeplotblank	0.36	0.00	0.36
nodeplotboot	0	0	0
nodeplotdefault	0	0	0
nsamples-methods	0.03	0.00	0.03
ntaxa-methods	0.00	0.02	0.01
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.18	0.00	0.19
phyloseq	0.05	0.00	0.05
phyloseq_to_deseq2	2.43	0.06	2.49
phyloseq_to_metagenomeSeq	2.00	0.03	2.03
plot_bar	3.54	0.02	3.98
plot_clusgap	6.59	0.12	6.74
plot_heatmap	7.16	0.03	7.19
plot_net	6.52	0.03	6.55
plot_network	3.77	0.00	3.79
plot_ordination	0.8	0.0	0.8
plot_phyloseq-methods	0.34	0.00	0.34
plot_richness	5.85	0.11	6.13
plot_scree	2.42	0.00	2.42
plot_tree	0.86	0.00	0.86
prune_samples-methods	0.55	0.03	0.57
prune_taxa-methods	0.06	0.00	0.06
psmelt	1.58	0.02	1.60
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.15	0.00	0.15
read_tree	0.16	0.00	0.16
read_tree_greengenes	0.03	0.00	0.03
reconcile_categories	0	0	0
refseq-methods	0.18	0.00	0.18
rm_outlierf	0.04	0.00	0.03
sample_data-methods	0.04	0.01	0.07
sample_names-methods	0	0	0
sample_sums	0.03	0.00	0.03
sample_variables	0.03	0.02	0.05
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	0.03	0.02	0.04
taxa_sums	0.03	0.01	0.05
threshrank	2.62	0.47	3.35
threshrankfun	0.08	0.00	0.08
tip_glom	1.11	0.00	1.10
topf	0.03	0.00	0.04
topk	0.03	0.00	0.03
topp	0.03	0.00	0.03
transformcounts	0.21	0.00	0.20
transpose-methods	1.7	0.3	2.0
tree_layout	0.71	0.00	0.72

BioC 3.3: CHECK report for phyloseq on moscato2

Summary

Command output