BioC 3.0: CHECK report for phyloseq on oaxaca

Package: phyloseq

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.10.0.tar.gz

StartedAt: 2015-04-10 02:08:31 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:17:53 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 561.5 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 --no-multiarch phyloseq_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/phyloseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.10.0’
* 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 ... [34s/35s] 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 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 ... 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 ... [96s/98s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 5.916  0.496   6.444
plot_net      6.051  0.147   6.271
plot_heatmap  5.460  0.254   5.765
threshrank    4.201  1.082   5.359
plot_clusgap  5.005  0.136   5.187
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [103s/104s]
 [103s/105s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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 ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
** 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 ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	4.082	0.223	4.368
JSD	0.001	0.000	0.001
UniFrac-methods	0.145	0.007	0.153
access	0.000	0.001	0.000
assign-otu_table	0.001	0.000	0.000
assign-phy_tree	0.046	0.004	0.050
assign-sample_data	0.841	0.022	0.881
assign-sample_names	0.010	0.008	0.018
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.004	0.009	0.012
assign-taxa_names	0.007	0.007	0.015
build_tax_table	0.016	0.001	0.017
capscale-phyloseq-methods	1.426	0.087	1.580
cca-rda-phyloseq-methods	0.001	0.000	0.001
data-GlobalPatterns	2.173	0.082	2.309
data-enterotype	2.788	0.028	2.821
data-esophagus	0.917	0.014	0.932
data-soilrep	2.263	0.134	2.410
distance	0.461	0.089	1.891
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.031	0.004	0.036
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.076	0.017	0.093
extract-methods	0.012	0.003	0.016
filter_taxa	0.255	0.035	0.290
filterfun_sample	0.026	0.000	0.026
gapstat_ord	2.608	0.043	2.678
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0.000	0.000	0.001
get_sample-methods	0.004	0.007	0.010
get_taxa-methods	0.004	0.006	0.009
get_taxa_unique	0.297	0.030	0.327
get_variable	0.229	0.011	0.240
getslots.phyloseq	0.227	0.020	0.247
import	0.001	0.000	0.000
import_RDP_otu	1.295	0.024	1.332
import_biom	0.185	0.002	0.214
import_env_file	0.000	0.000	0.001
import_mothur	0.001	0.000	0.002
import_mothur_dist	0.001	0.000	0.001
import_pyrotagger_tab	0.000	0.001	0.000
import_qiime	0.664	0.014	0.678
import_qiime_otu_tax	0.550	0.052	0.602
import_qiime_sample_data	0.028	0.001	0.030
import_usearch_uc	0.019	0.004	0.024
index_reorder	0	0	0
intersect_taxa	0.000	0.000	0.001
make_network	4.397	0.086	4.505
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.001	0.001
merge_samples-methods	1.329	0.211	1.542
merge_taxa-methods	0.059	0.006	0.065
microbio_me_qiime	0.772	0.017	0.824
mt-methods	1.716	0.027	1.745
nodeplotblank	0.471	0.004	0.477
nodeplotboot	0.003	0.000	0.002
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.025	0.003	0.029
ntaxa-methods	0.004	0.003	0.007
ordinate	0.001	0.000	0.001
otu_table-methods	0.001	0.000	0.001
parseTaxonomy-functions	0.002	0.001	0.002
phy_tree-methods	0.234	0.015	0.249
phyloseq	0.025	0.005	0.030
phyloseq_to_deseq2	0.808	0.064	0.873
plot_bar	3.268	0.135	3.418
plot_clusgap	5.005	0.136	5.187
plot_heatmap	5.460	0.254	5.765
plot_net	6.051	0.147	6.271
plot_network	3.455	0.045	3.522
plot_ordination	1.034	0.076	1.140
plot_phyloseq-methods	0.356	0.007	0.363
plot_richness	5.916	0.496	6.444
plot_scree	2.182	0.082	2.361
plot_tree	0.877	0.010	0.901
prune_samples-methods	1.186	0.117	1.306
prune_taxa-methods	0.036	0.003	0.040
psmelt	1.245	0.119	1.374
rank_names	0.029	0.006	0.034
rarefy_even_depth	0.090	0.005	0.095
read_tree	0.151	0.002	0.152
read_tree_greengenes	0.056	0.001	0.057
reconcile_categories	0.001	0.001	0.001
refseq-methods	0.218	0.012	0.232
rm_outlierf	0.019	0.001	0.021
sample_data-methods	0.057	0.008	0.065
sample_names-methods	0.003	0.005	0.008
sample_sums	0.034	0.013	0.047
sample_variables	0.028	0.006	0.049
show-methods	0.001	0.000	0.000
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0.000	0.000	0.001
subset_samples-methods	0.001	0.000	0.000
subset_taxa-methods	0.001	0.000	0.000
tax_glom	0.001	0.001	0.001
tax_table-methods	0.001	0.000	0.001
taxa_names-methods	0.024	0.006	0.030
taxa_sums	0.039	0.017	0.056
threshrank	4.201	1.082	5.359
threshrankfun	0.057	0.004	0.060
tip_glom	0.940	0.006	0.958
topf	0.027	0.001	0.028
topk	0.027	0.000	0.027
topp	0.020	0.001	0.025
transformcounts	0.120	0.003	0.149
transpose-methods	0.986	0.641	1.647
tree_layout	0.725	0.014	0.747