BioC 3.5: CHECK report for phyloseq on tokay2

Package: phyloseq

Version: 1.20.0

Command: rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.20.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.20.0.tar.gz

StartedAt: 2017-08-16 01:56:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:04:29 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 498.7 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf phyloseq.buildbin-libdir phyloseq.Rcheck && mkdir phyloseq.buildbin-libdir phyloseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.20.0.tar.gz >phyloseq.Rcheck\00install.out 2>&1 && cp phyloseq.Rcheck\00install.out phyloseq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.20.0'
* 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
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
      user system elapsed
DPCoA 5.97   0.06    6.03
* 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
  'C:/Users/biocbuild/bbs-3.5-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_1.20.0.zip
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	4.04	0.05	4.09
JSD	0	0	0
UniFrac-methods	0.33	0.00	0.33
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.28	0.00	0.28
assign-sample_data	0.45	0.02	0.47
assign-sample_names	0.02	0.00	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0.01	0.00	0.02
build_tax_table	0.25	0.00	0.25
capscale-phyloseq-methods	0.63	0.06	0.69
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	1.58	0.03	1.60
data-enterotype	1.25	0.01	1.27
data-esophagus	0.39	0.00	0.39
data-soilrep	1.93	0.08	2.02
distance	0.41	0.02	1.75
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.06	0.00	0.06
export_env_file	0	0	0
export_mothur_dist	0.11	0.00	0.11
extract-methods	0	0	0
filter_taxa	1.25	0.01	1.27
filterfun_sample	0.02	0.00	0.02
gapstat_ord	1.40	0.02	1.42
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	0.01
get_taxa_unique	0.24	0.00	0.24
get_variable	0.15	0.04	0.20
getslots.phyloseq	0.21	0.00	0.20
import	0	0	0
import_RDP_otu	1.53	0.02	1.55
import_biom	0.48	0.00	0.49
import_env_file	0	0	0
import_mothur	0.02	0.00	0.01
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.90	0.00	0.91
import_qiime_otu_tax	0.52	0.01	0.53
import_qiime_sample_data	0.01	0.00	0.01
import_uparse	0	0	0
import_usearch_uc	0.02	0.00	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.11	0.03	2.14
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.58	0.08	0.66
merge_taxa-methods	0.06	0.00	0.06
microbio_me_qiime	0.91	0.03	1.00
mt-methods	2.28	0.02	2.30
nodeplotblank	0.43	0.00	0.43
nodeplotboot	0.02	0.00	0.02
nodeplotdefault	0.02	0.00	0.02
nsamples-methods	0.01	0.00	0.01
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0.02	0.00	0.02
phy_tree-methods	0.18	0.00	0.18
phyloseq	0.02	0.00	0.02
phyloseq_to_deseq2	2.77	0.11	2.87
phyloseq_to_metagenomeSeq	1.24	0.08	1.31
plot_bar	1.84	0.04	1.89
plot_clusgap	3.66	0.16	3.83
plot_heatmap	3.84	0.06	3.91
plot_net	4.02	0.03	4.03
plot_network	1.76	0.02	1.78
plot_ordination	0.56	0.00	0.56
plot_phyloseq-methods	0.3	0.0	0.3
plot_richness	4.27	0.22	4.48
plot_scree	2.17	0.05	2.22
plot_tree	0.65	0.00	0.66
prune_samples-methods	0.89	0.06	0.95
prune_taxa-methods	0.04	0.00	0.03
psmelt	0.67	0.00	0.68
rank_names	0.03	0.00	0.03
rarefy_even_depth	0.09	0.00	0.09
read_tree	0.05	0.00	0.05
read_tree_greengenes	0.03	0.00	0.03
reconcile_categories	0	0	0
refseq-methods	0.19	0.00	0.19
rm_outlierf	0.03	0.00	0.03
sample_data-methods	0.05	0.00	0.04
sample_names-methods	0.00	0.01	0.02
sample_sums	0.01	0.02	0.03
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	0.02	0.01	0.03
taxa_sums	0.03	0.00	0.03
threshrank	2.75	0.27	3.02
threshrankfun	0.06	0.00	0.06
tip_glom	0.64	0.00	0.64
topf	0.02	0.00	0.01
topk	0.01	0.00	0.02
topp	0.02	0.00	0.02
transformcounts	0.11	0.00	0.11
transpose-methods	0.94	0.23	1.17
tree_layout	0.61	0.05	0.65

name	user	system	elapsed
DPCoA	5.97	0.06	6.03
JSD	0	0	0
UniFrac-methods	0.59	0.00	0.64
access	0	0	0
assign-otu_table	0	0	0
assign-phy_tree	0.25	0.00	0.25
assign-sample_data	0.16	0.02	0.17
assign-sample_names	0.00	0.01	0.01
assign-tax_table	0	0	0
assign-taxa_are_rows	0	0	0
assign-taxa_names	0	0	0
build_tax_table	0.03	0.00	0.03
capscale-phyloseq-methods	1.20	0.01	1.22
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0	0	0
data-GlobalPatterns	2.3	0.0	2.3
data-enterotype	1.78	0.03	1.81
data-esophagus	0.56	0.00	0.56
data-soilrep	2.24	0.05	2.28
distance	0.26	0.03	0.30
distanceMethodList	0	0	0
envHash2otu_table	0	0	0
estimate_richness	0.05	0.02	0.06
export_env_file	0	0	0
export_mothur_dist	0.06	0.00	0.06
extract-methods	0.02	0.00	0.02
filter_taxa	1.04	0.01	1.06
filterfun_sample	0.03	0.00	0.03
gapstat_ord	1.64	0.04	1.68
genefilter_sample-methods	0	0	0
get.component.classes	0	0	0
get_sample-methods	0	0	0
get_taxa-methods	0.02	0.00	0.01
get_taxa_unique	0.28	0.00	0.28
get_variable	0.19	0.00	0.19
getslots.phyloseq	0.19	0.00	0.19
import	0	0	0
import_RDP_otu	1.22	0.00	1.22
import_biom	0.36	0.00	0.38
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	0.88	0.00	0.87
import_qiime_otu_tax	0.63	0.01	0.64
import_qiime_sample_data	0.02	0.00	0.02
import_uparse	0	0	0
import_usearch_uc	0.00	0.02	0.02
index_reorder	0	0	0
intersect_taxa	0	0	0
make_network	2.50	0.03	2.53
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0	0	0
merge_samples-methods	0.71	0.08	0.78
merge_taxa-methods	0.07	0.00	0.08
microbio_me_qiime	0.99	0.00	1.14
mt-methods	1.55	0.00	1.55
nodeplotblank	0.65	0.00	0.67
nodeplotboot	0.03	0.00	0.03
nodeplotdefault	0	0	0
nsamples-methods	0.03	0.00	0.03
ntaxa-methods	0	0	0
ordinate	0	0	0
otu_table-methods	0	0	0
parseTaxonomy-functions	0	0	0
phy_tree-methods	0.19	0.00	0.19
phyloseq	0.02	0.00	0.02
phyloseq_to_deseq2	2.86	0.03	2.89
phyloseq_to_metagenomeSeq	1.63	0.03	1.66
plot_bar	1.93	0.01	1.95
plot_clusgap	3.79	0.11	3.91
plot_heatmap	4.81	0.03	4.84
plot_net	4.39	0.02	4.41
plot_network	2.05	0.00	2.05
plot_ordination	1.18	0.00	1.18
plot_phyloseq-methods	0.19	0.00	0.19
plot_richness	4.38	0.11	4.48
plot_scree	2.50	0.03	2.54
plot_tree	0.76	0.03	0.76
prune_samples-methods	1.03	0.02	1.05
prune_taxa-methods	0.03	0.01	0.05
psmelt	0.64	0.00	0.64
rank_names	0.02	0.00	0.02
rarefy_even_depth	0.18	0.00	0.18
read_tree	0.1	0.0	0.1
read_tree_greengenes	0.03	0.00	0.04
reconcile_categories	0	0	0
refseq-methods	0.24	0.00	0.23
rm_outlierf	0.05	0.00	0.05
sample_data-methods	0.06	0.00	0.06
sample_names-methods	0	0	0
sample_sums	0.04	0.00	0.05
sample_variables	0.04	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	0.02	0.00	0.02
taxa_sums	0.03	0.02	0.05
threshrank	1.69	0.41	2.09
threshrankfun	0.09	0.00	0.09
tip_glom	0.94	0.00	0.94
topf	0.01	0.00	0.02
topk	0.01	0.00	0.02
topp	0.02	0.00	0.01
transformcounts	0.11	0.00	0.11
transpose-methods	0.83	0.42	1.25
tree_layout	0.73	0.02	0.73