BioC 3.5: CHECK report for phyloseq on oaxaca

Package: phyloseq

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.19.2.tar.gz

StartedAt: 2017-03-04 07:04:18 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:09:15 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 297.1 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_1.19.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.19.2’
* 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
DPCoA 5.015  0.155   5.173
* 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-3.5-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	5.015	0.155	5.173
JSD	0.000	0.001	0.000
UniFrac-methods	0.87	0.01	0.88
access	0.000	0.000	0.001
assign-otu_table	0	0	0
assign-phy_tree	0.208	0.006	0.214
assign-sample_data	0.396	0.015	0.410
assign-sample_names	0.010	0.009	0.019
assign-tax_table	0.001	0.001	0.001
assign-taxa_are_rows	0.003	0.010	0.013
assign-taxa_names	0.009	0.009	0.019
build_tax_table	0.040	0.001	0.040
capscale-phyloseq-methods	1.091	0.077	1.169
cca-rda-phyloseq-methods	0	0	0
chunkReOrder	0.001	0.000	0.001
data-GlobalPatterns	1.886	0.077	1.963
data-enterotype	1.755	0.017	1.773
data-esophagus	0.629	0.007	0.636
data-soilrep	1.959	0.105	2.065
distance	0.258	0.023	1.312
distanceMethodList	0.000	0.000	0.001
envHash2otu_table	0.001	0.000	0.000
estimate_richness	0.039	0.002	0.041
export_env_file	0.001	0.000	0.000
export_mothur_dist	0.064	0.012	0.076
extract-methods	0.006	0.002	0.007
filter_taxa	0.901	0.034	0.934
filterfun_sample	0.041	0.001	0.041
gapstat_ord	1.627	0.033	1.661
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.001	0.000	0.000
get_sample-methods	0.002	0.002	0.006
get_taxa-methods	0.004	0.004	0.009
get_taxa_unique	0.188	0.018	0.217
get_variable	0.135	0.005	0.140
getslots.phyloseq	0.213	0.012	0.226
import	0.001	0.000	0.001
import_RDP_otu	1.002	0.025	1.027
import_biom	0.378	0.013	0.391
import_env_file	0.001	0.000	0.001
import_mothur	0.001	0.000	0.000
import_mothur_dist	0.000	0.000	0.001
import_pyrotagger_tab	0.000	0.001	0.001
import_qiime	0.934	0.017	0.954
import_qiime_otu_tax	0.655	0.035	0.690
import_qiime_sample_data	0.016	0.001	0.016
import_uparse	0.000	0.000	0.001
import_usearch_uc	0.013	0.002	0.016
index_reorder	0.001	0.000	0.000
intersect_taxa	0.001	0.000	0.000
make_network	2.636	0.071	2.709
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.001	0.002
merge_samples-methods	0.578	0.123	0.702
merge_taxa-methods	0.097	0.005	0.101
microbio_me_qiime	0.944	0.022	1.032
mt-methods	1.642	0.024	1.668
nodeplotblank	0.794	0.013	0.824
nodeplotboot	0.025	0.001	0.025
nodeplotdefault	0	0	0
nsamples-methods	0.020	0.004	0.024
ntaxa-methods	0.004	0.004	0.009
ordinate	0.001	0.000	0.001
otu_table-methods	0.001	0.000	0.001
parseTaxonomy-functions	0.003	0.000	0.004
phy_tree-methods	0.232	0.014	0.247
phyloseq	0.026	0.005	0.032
phyloseq_to_deseq2	2.535	0.087	2.624
phyloseq_to_metagenomeSeq	1.209	0.088	1.296
plot_bar	2.172	0.106	2.279
plot_clusgap	4.215	0.148	4.381
plot_heatmap	4.508	0.212	4.723
plot_net	2.956	0.131	3.127
plot_network	1.652	0.034	1.688
plot_ordination	0.738	0.056	0.795
plot_phyloseq-methods	0.235	0.003	0.239
plot_richness	4.365	0.392	4.854
plot_scree	2.859	0.057	2.919
plot_tree	0.589	0.008	0.599
prune_samples-methods	0.470	0.086	0.556
prune_taxa-methods	0.046	0.004	0.081
psmelt	0.729	0.073	0.802
rank_names	0.020	0.003	0.023
rarefy_even_depth	0.099	0.002	0.101
read_tree	0.074	0.001	0.076
read_tree_greengenes	0.026	0.000	0.027
reconcile_categories	0	0	0
refseq-methods	0.135	0.009	0.144
rm_outlierf	0.034	0.003	0.036
sample_data-methods	0.044	0.004	0.049
sample_names-methods	0.002	0.004	0.006
sample_sums	0.024	0.008	0.032
sample_variables	0.020	0.004	0.024
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0	0	0
subset_ord_plot	0.000	0.000	0.001
subset_samples-methods	0	0	0
subset_taxa-methods	0.001	0.000	0.000
tax_glom	0.000	0.000	0.001
tax_table-methods	0	0	0
taxa_names-methods	0.024	0.003	0.027
taxa_sums	0.029	0.010	0.038
threshrank	2.310	0.794	3.109
threshrankfun	0.061	0.012	0.073
tip_glom	0.880	0.023	0.904
topf	0.019	0.001	0.019
topk	0.017	0.001	0.017
topp	0.018	0.000	0.019
transformcounts	0.125	0.004	0.129
transpose-methods	0.863	0.544	1.409
tree_layout	0.785	0.022	0.839