BioC 3.3: CHECK report for phyloseq on oaxaca

Package: phyloseq

Version: 1.16.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.16.2.tar.gz

StartedAt: 2016-10-13 05:01:20 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:06:37 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 317.6 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.16.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/phyloseq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘phyloseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.2Mb
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 4.715  0.394   5.115
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	3.450	0.174	3.722
JSD	0.001	0.000	0.000
UniFrac-methods	0.143	0.011	0.155
access	0.001	0.000	0.001
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.053	0.008	0.061
assign-sample_data	0.620	0.027	0.648
assign-sample_names	0.008	0.004	0.012
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.003	0.003	0.007
assign-taxa_names	0.009	0.004	0.013
build_tax_table	0.015	0.000	0.015
capscale-phyloseq-methods	0.653	0.060	0.715
cca-rda-phyloseq-methods	0.000	0.000	0.001
chunkReOrder	0.002	0.000	0.001
data-GlobalPatterns	1.339	0.063	1.404
data-enterotype	2.078	0.040	2.119
data-esophagus	0.746	0.014	0.760
data-soilrep	1.580	0.126	1.708
distance	0.204	0.028	1.408
distanceMethodList	0.000	0.000	0.001
envHash2otu_table	0.000	0.000	0.001
estimate_richness	0.030	0.002	0.032
export_env_file	0.001	0.000	0.000
export_mothur_dist	0.104	0.017	0.122
extract-methods	0.009	0.001	0.011
filter_taxa	1.578	0.035	1.614
filterfun_sample	0.023	0.001	0.024
gapstat_ord	2.162	0.046	2.232
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.001	0.000	0.000
get_sample-methods	0.004	0.003	0.007
get_taxa-methods	0.004	0.003	0.007
get_taxa_unique	0.275	0.023	0.298
get_variable	0.230	0.016	0.245
getslots.phyloseq	0.209	0.013	0.223
import	0	0	0
import_RDP_otu	0.725	0.027	0.755
import_biom	0.211	0.003	0.215
import_env_file	0.001	0.000	0.000
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.000	0.000	0.001
import_pyrotagger_tab	0.000	0.000	0.001
import_qiime	0.622	0.012	0.634
import_qiime_otu_tax	0.545	0.057	0.601
import_qiime_sample_data	0.020	0.001	0.021
import_uparse	0.000	0.000	0.001
import_usearch_uc	0.017	0.004	0.021
index_reorder	0.001	0.000	0.000
intersect_taxa	0.000	0.000	0.001
make_network	3.446	0.070	3.517
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.002	0.000	0.001
merge_samples-methods	1.219	0.148	1.370
merge_taxa-methods	0.063	0.005	0.068
microbio_me_qiime	0.724	0.015	0.782
mt-methods	1.866	0.029	1.897
nodeplotblank	0.338	0.009	0.347
nodeplotboot	0.002	0.000	0.002
nodeplotdefault	0.001	0.001	0.001
nsamples-methods	0.031	0.008	0.039
ntaxa-methods	0.004	0.008	0.012
ordinate	0.000	0.000	0.001
otu_table-methods	0	0	0
parseTaxonomy-functions	0.003	0.001	0.003
phy_tree-methods	0.208	0.020	0.228
phyloseq	0.032	0.010	0.041
phyloseq_to_deseq2	2.239	0.083	2.326
phyloseq_to_metagenomeSeq	1.840	0.118	1.959
plot_bar	2.448	0.103	2.552
plot_clusgap	4.356	0.135	4.509
plot_heatmap	4.318	0.189	4.519
plot_net	4.544	0.120	4.692
plot_network	2.739	0.034	2.777
plot_ordination	0.760	0.062	0.823
plot_phyloseq-methods	0.280	0.003	0.285
plot_richness	4.715	0.394	5.115
plot_scree	2.043	0.064	2.913
plot_tree	0.671	0.006	0.677
prune_samples-methods	0.868	0.087	0.956
prune_taxa-methods	0.038	0.003	0.042
psmelt	0.824	0.088	0.914
rank_names	0.036	0.011	0.047
rarefy_even_depth	0.117	0.008	0.124
read_tree	0.151	0.001	0.152
read_tree_greengenes	0.049	0.000	0.048
reconcile_categories	0.001	0.001	0.001
refseq-methods	0.192	0.016	0.208
rm_outlierf	0.024	0.000	0.025
sample_data-methods	0.060	0.010	0.071
sample_names-methods	0.003	0.009	0.012
sample_sums	0.032	0.021	0.053
sample_variables	0.028	0.011	0.040
show-methods	0	0	0
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0	0	0
subset_samples-methods	0.001	0.000	0.000
subset_taxa-methods	0.001	0.000	0.001
tax_glom	0.001	0.001	0.001
tax_table-methods	0.001	0.000	0.001
taxa_names-methods	0.029	0.009	0.038
taxa_sums	0.050	0.022	0.071
threshrank	3.364	0.924	4.291
threshrankfun	0.056	0.004	0.059
tip_glom	0.840	0.005	0.848
topf	0.019	0.000	0.020
topk	0.017	0.001	0.018
topp	0.019	0.001	0.019
transformcounts	0.153	0.004	0.157
transpose-methods	0.921	0.591	1.512
tree_layout	0.757	0.009	0.786