BioC 3.5: CHECK report for phyloseq on malbec2

Package: phyloseq

Version: 1.20.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.20.0.tar.gz

StartedAt: 2017-08-16 01:16:15 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:20:19 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 244.4 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* 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
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	4.036	0.028	4.068
JSD	0	0	0
UniFrac-methods	0.388	0.004	0.390
access	0.000	0.000	0.001
assign-otu_table	0	0	0
assign-phy_tree	0.192	0.000	0.191
assign-sample_data	0.488	0.004	0.493
assign-sample_names	0.004	0.000	0.006
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.004	0.000	0.003
assign-taxa_names	0.004	0.000	0.006
build_tax_table	0.024	0.000	0.022
capscale-phyloseq-methods	0.644	0.016	0.660
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0.000	0.004	0.001
data-GlobalPatterns	1.532	0.004	1.540
data-enterotype	1.672	0.000	1.674
data-esophagus	0.460	0.000	0.463
data-soilrep	0.996	0.004	1.001
distance	0.204	0.032	1.093
distanceMethodList	0.000	0.000	0.001
envHash2otu_table	0.004	0.000	0.001
estimate_richness	0.064	0.008	0.072
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.084	0.028	0.112
extract-methods	0.008	0.000	0.010
filter_taxa	1.384	0.052	1.439
filterfun_sample	0.032	0.000	0.033
gapstat_ord	1.368	0.012	1.381
genefilter_sample-methods	0.004	0.000	0.001
get.component.classes	0.000	0.000	0.001
get_sample-methods	0.004	0.000	0.003
get_taxa-methods	0.004	0.000	0.002
get_taxa_unique	0.204	0.004	0.210
get_variable	0.164	0.000	0.162
getslots.phyloseq	0.160	0.000	0.161
import	0	0	0
import_RDP_otu	0.348	0.008	0.356
import_biom	0.332	0.000	0.330
import_env_file	0	0	0
import_mothur	0.000	0.000	0.001
import_mothur_dist	0.004	0.000	0.000
import_pyrotagger_tab	0	0	0
import_qiime	0.832	0.036	0.866
import_qiime_otu_tax	0.548	0.020	0.568
import_qiime_sample_data	0.012	0.000	0.012
import_uparse	0.000	0.000	0.001
import_usearch_uc	0.012	0.000	0.011
index_reorder	0.004	0.000	0.001
intersect_taxa	0.000	0.000	0.001
make_network	1.912	0.004	1.917
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.004	0.000	0.001
merge_samples-methods	0.648	0.000	0.648
merge_taxa-methods	0.064	0.000	0.064
microbio_me_qiime	0.636	0.068	0.716
mt-methods	1.264	0.000	1.265
nodeplotblank	0.696	0.000	0.544
nodeplotboot	0.020	0.000	0.022
nodeplotdefault	0	0	0
nsamples-methods	0.016	0.000	0.018
ntaxa-methods	0.000	0.000	0.003
ordinate	0.000	0.000	0.001
otu_table-methods	0.000	0.000	0.001
parseTaxonomy-functions	0.004	0.000	0.002
phy_tree-methods	0.156	0.000	0.157
phyloseq	0.016	0.000	0.017
phyloseq_to_deseq2	2.280	0.048	2.330
phyloseq_to_metagenomeSeq	1.356	0.012	1.370
plot_bar	1.656	0.008	1.666
plot_clusgap	3.340	0.016	3.366
plot_heatmap	3.764	0.004	3.770
plot_net	3.220	0.008	2.975
plot_network	1.528	0.000	1.529
plot_ordination	0.548	0.004	0.553
plot_phyloseq-methods	0.288	0.004	0.205
plot_richness	3.440	0.008	3.449
plot_scree	2.204	0.004	2.210
plot_tree	0.648	0.004	0.488
prune_samples-methods	0.372	0.000	0.373
prune_taxa-methods	0.032	0.004	0.036
psmelt	0.648	0.004	0.652
rank_names	0.020	0.000	0.022
rarefy_even_depth	0.096	0.000	0.096
read_tree	0.068	0.000	0.069
read_tree_greengenes	0.024	0.000	0.023
reconcile_categories	0.004	0.000	0.001
refseq-methods	0.140	0.004	0.148
rm_outlierf	0.024	0.000	0.024
sample_data-methods	0.064	0.000	0.064
sample_names-methods	0.004	0.000	0.003
sample_sums	0.024	0.000	0.026
sample_variables	0.020	0.000	0.022
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	0.000	0.000	0.001
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.02	0.00	0.02
taxa_sums	0.032	0.000	0.029
threshrank	1.908	0.356	2.265
threshrankfun	0.064	0.000	0.063
tip_glom	1.372	0.008	1.108
topf	0.012	0.000	0.010
topk	0.012	0.000	0.011
topp	0.012	0.000	0.011
transformcounts	0.080	0.000	0.078
transpose-methods	0.448	0.228	0.675
tree_layout	0.540	0.000	0.526