BioC 3.0: CHECK report for phyloseq on perceval

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 04:47:10 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:59:24 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 733.4 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-darwin10.8.0 (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 ... [46s/52s] 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
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’
JSD: no visible binding for global variable ‘i’
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 ... [120s/123s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 7.026  0.788   8.176
plot_heatmap  7.059  0.492   7.621
plot_clusgap  6.912  0.273   7.249
plot_net      6.477  0.229   6.767
threshrank    5.071  1.578   6.873
DPCoA         5.724  0.330   6.081
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [125s/127s]
 [126s/128s] 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	5.724	0.330	6.081
JSD	0.000	0.001	0.001
UniFrac-methods	0.206	0.058	0.264
access	0.000	0.000	0.001
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.057	0.004	0.060
assign-sample_data	1.736	0.038	1.775
assign-sample_names	0.012	0.003	0.015
assign-tax_table	0.001	0.001	0.001
assign-taxa_are_rows	0.004	0.003	0.007
assign-taxa_names	0.011	0.004	0.015
build_tax_table	0.019	0.000	0.020
capscale-phyloseq-methods	1.754	0.122	1.883
cca-rda-phyloseq-methods	0.001	0.000	0.000
data-GlobalPatterns	3.013	0.134	3.157
data-enterotype	2.414	0.040	2.465
data-esophagus	0.896	0.025	0.922
data-soilrep	3.882	0.252	4.148
distance	0.476	0.088	1.267
envHash2otu_table	0.000	0.000	0.001
estimate_richness	0.031	0.004	0.034
export_env_file	0.001	0.000	0.000
export_mothur_dist	0.096	0.030	0.500
extract-methods	0.014	0.003	0.016
filter_taxa	0.304	0.033	0.337
filterfun_sample	0.032	0.001	0.032
gapstat_ord	3.060	0.076	3.155
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.000	0.000	0.001
get_sample-methods	0.006	0.008	0.014
get_taxa-methods	0.005	0.005	0.010
get_taxa_unique	0.271	0.034	0.306
get_variable	0.204	0.017	0.222
getslots.phyloseq	0.224	0.028	0.253
import	0.000	0.000	0.001
import_RDP_otu	1.764	0.041	1.806
import_biom	0.223	0.011	0.251
import_env_file	0.001	0.000	0.001
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.001	0.001	0.000
import_pyrotagger_tab	0.001	0.000	0.000
import_qiime	1.145	0.006	1.151
import_qiime_otu_tax	0.958	0.070	1.030
import_qiime_sample_data	0.032	0.002	0.034
import_usearch_uc	0.024	0.006	0.029
index_reorder	0.001	0.000	0.000
intersect_taxa	0.000	0.000	0.002
make_network	4.494	0.159	4.737
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	2.425	0.351	2.779
merge_taxa-methods	0.067	0.003	0.070
microbio_me_qiime	0.813	0.032	0.998
mt-methods	2.769	0.051	2.838
nodeplotblank	0.424	0.007	0.450
nodeplotboot	0.003	0.001	0.004
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.025	0.003	0.028
ntaxa-methods	0.005	0.003	0.008
ordinate	0.000	0.000	0.001
otu_table-methods	0.001	0.000	0.001
parseTaxonomy-functions	0.003	0.000	0.003
phy_tree-methods	0.208	0.023	0.231
phyloseq	0.027	0.008	0.035
phyloseq_to_deseq2	1.099	0.098	1.198
plot_bar	3.417	0.192	3.751
plot_clusgap	6.912	0.273	7.249
plot_heatmap	7.059	0.492	7.621
plot_net	6.477	0.229	6.767
plot_network	3.456	0.078	3.623
plot_ordination	1.002	0.117	1.130
plot_phyloseq-methods	0.336	0.005	0.349
plot_richness	7.026	0.788	8.176
plot_scree	2.874	0.119	3.052
plot_tree	0.861	0.016	0.896
prune_samples-methods	0.850	0.183	1.035
prune_taxa-methods	0.035	0.004	0.046
psmelt	1.251	0.193	1.454
rank_names	0.025	0.008	0.033
rarefy_even_depth	0.094	0.004	0.099
read_tree	0.173	0.009	0.182
read_tree_greengenes	0.051	0.001	0.053
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.199	0.020	0.220
rm_outlierf	0.021	0.001	0.022
sample_data-methods	0.063	0.013	0.076
sample_names-methods	0.003	0.008	0.012
sample_sums	0.031	0.020	0.053
sample_variables	0.026	0.012	0.039
show-methods	0.001	0.000	0.001
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	0.001
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.001	0.000	0.001
tax_table-methods	0.001	0.000	0.001
taxa_names-methods	0.027	0.010	0.037
taxa_sums	0.041	0.028	0.070
threshrank	5.071	1.578	6.873
threshrankfun	0.059	0.004	0.063
tip_glom	0.974	0.009	1.074
topf	0.026	0.001	0.028
topk	0.037	0.001	0.038
topp	0.026	0.001	0.027
transformcounts	0.137	0.004	0.141
transpose-methods	1.126	0.859	1.987
tree_layout	0.839	0.020	0.890