BioC 3.1: CHECK report for phyloseq on zin2

Package: phyloseq

Version: 1.12.2

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.12.2.tar.gz

StartedAt: 2015-10-09 04:17:32 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:22:46 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 314.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: phyloseq.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.12.2’
* 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 ... [18s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘JSD.pair’
* 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
JSD: no visible binding for global variable ‘i’
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_usearch_uc: no visible global function definition for ‘:=’
import_usearch_uc: no visible binding for global variable ‘read’
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’
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 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
  ‘vertex’
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 : links_to_ggplot: no visible binding for global variable ‘x’
plot_net : links_to_ggplot: no visible binding for global variable ‘y’
plot_net : links_to_ggplot: no visible binding for global variable
  ‘xend’
plot_net : links_to_ggplot: 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 ‘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’
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’
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
  binding for global variable ‘X0’
plot_phyloseq,phyloseq: no visible binding for global variable
  ‘esophagus’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘dist’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [63s/63s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [68s/68s]
 [68s/68s] 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.373	0.040	3.422
JSD	0	0	0
UniFrac-methods	0.107	0.000	0.106
access	0.001	0.000	0.001
assign-otu_table	0.001	0.000	0.000
assign-phy_tree	0.038	0.000	0.038
assign-sample_data	0.450	0.004	0.454
assign-sample_names	0.007	0.000	0.008
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.002	0.000	0.003
assign-taxa_names	0.007	0.000	0.007
build_tax_table	0.012	0.000	0.011
capscale-phyloseq-methods	0.667	0.000	0.667
cca-rda-phyloseq-methods	0.001	0.000	0.001
data-GlobalPatterns	1.401	0.004	1.404
data-enterotype	1.933	0.000	1.937
data-esophagus	0.592	0.000	0.592
data-soilrep	1.662	0.004	1.668
distance	0.180	0.021	0.482
envHash2otu_table	0.000	0.000	0.001
estimate_richness	0.022	0.004	0.026
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.073	0.020	0.092
extract-methods	0.009	0.000	0.009
filter_taxa	0.164	0.012	0.177
filterfun_sample	0.019	0.000	0.020
gapstat_ord	1.508	0.016	1.524
genefilter_sample-methods	0	0	0
get.component.classes	0.001	0.000	0.001
get_sample-methods	0.003	0.000	0.003
get_taxa-methods	0.004	0.000	0.004
get_taxa_unique	0.223	0.012	0.235
get_variable	0.173	0.000	0.173
getslots.phyloseq	0.157	0.004	0.161
import	0.001	0.000	0.000
import_RDP_otu	0.929	0.028	0.956
import_biom	0.136	0.000	0.148
import_env_file	0	0	0
import_mothur	0.001	0.000	0.001
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.645	0.000	0.652
import_qiime_otu_tax	0.591	0.036	0.630
import_qiime_sample_data	0.019	0.000	0.019
import_usearch_uc	0.012	0.004	0.016
index_reorder	0	0	0
intersect_taxa	0.000	0.000	0.001
make_network	3.200	0.020	3.222
merge_phyloseq	0.001	0.000	0.000
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.889	0.008	0.904
merge_taxa-methods	0.053	0.000	0.053
microbio_me_qiime	0.536	0.075	0.614
mt-methods	1.590	0.004	1.595
nodeplotblank	0.344	0.000	0.345
nodeplotboot	0.001	0.000	0.002
nodeplotdefault	0.001	0.000	0.000
nsamples-methods	0.026	0.000	0.027
ntaxa-methods	0.004	0.000	0.004
ordinate	0.001	0.000	0.000
otu_table-methods	0.000	0.000	0.001
parseTaxonomy-functions	0.003	0.000	0.002
phy_tree-methods	0.177	0.000	0.178
phyloseq	0.025	0.000	0.025
phyloseq_to_deseq2	0.783	0.040	0.823
plot_bar	1.732	0.004	1.748
plot_clusgap	4.506	0.024	4.558
plot_heatmap	3.316	0.008	3.323
plot_net	4.734	0.012	4.743
plot_network	2.212	0.000	2.210
plot_ordination	0.623	0.000	0.622
plot_phyloseq-methods	0.225	0.000	0.225
plot_richness	4.077	0.008	4.082
plot_scree	1.545	0.004	1.547
plot_tree	0.598	0.000	0.598
prune_samples-methods	0.541	0.004	0.545
prune_taxa-methods	0.03	0.00	0.03
psmelt	0.808	0.008	0.815
rank_names	0.023	0.000	0.024
rarefy_even_depth	0.083	0.000	0.083
read_tree	0.126	0.000	0.126
read_tree_greengenes	0.034	0.004	0.038
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.152	0.004	0.156
rm_outlierf	0.014	0.000	0.014
sample_data-methods	0.043	0.000	0.042
sample_names-methods	0.002	0.000	0.003
sample_sums	0.024	0.004	0.027
sample_variables	0.023	0.000	0.024
show-methods	0	0	0
splat.phyloseq.objects	0.001	0.000	0.000
subset_ord_plot	0.001	0.000	0.000
subset_samples-methods	0.000	0.004	0.001
subset_taxa-methods	0	0	0
tax_glom	0	0	0
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.019	0.004	0.023
taxa_sums	0.030	0.004	0.032
threshrank	2.846	0.512	3.375
threshrankfun	0.057	0.000	0.057
tip_glom	0.732	0.000	0.746
topf	0.023	0.000	0.023
topk	0.014	0.000	0.015
topp	0.016	0.000	0.015
transformcounts	0.113	0.000	0.119
transpose-methods	0.673	0.368	1.043
tree_layout	0.518	0.000	0.533