BioC 3.2: CHECK report for phyloseq on oaxaca

Package: phyloseq

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.14.0.tar.gz

StartedAt: 2015-10-27 06:32:06 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:37:59 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 352.7 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.0’
* 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 ... [18s/19s] 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.
* 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’
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’
JSD,matrix: no visible binding for global variable ‘i’
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 ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 4.558  0.468   5.047
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [82s/82s]
 [82s/83s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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.
** 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.
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.663	0.230	3.955
JSD	0.001	0.000	0.001
UniFrac-methods	0.148	0.007	0.273
access	0.000	0.000	0.001
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.046	0.004	0.050
assign-sample_data	0.374	0.020	0.394
assign-sample_names	0.007	0.001	0.008
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.003	0.001	0.003
assign-taxa_names	0.007	0.002	0.008
build_tax_table	0.018	0.001	0.018
capscale-phyloseq-methods	0.662	0.051	0.714
cca-rda-phyloseq-methods	0.000	0.000	0.001
chunkReOrder	0.001	0.001	0.001
data-GlobalPatterns	1.604	0.100	1.704
data-enterotype	1.805	0.041	1.872
data-esophagus	0.758	0.007	0.766
data-soilrep	1.553	0.147	1.705
distance	0.192	0.023	0.976
distanceMethodList	0.000	0.000	0.001
envHash2otu_table	0.001	0.001	0.001
estimate_richness	0.031	0.002	0.033
export_env_file	0	0	0
export_mothur_dist	0.091	0.015	0.106
extract-methods	0.010	0.002	0.012
filter_taxa	1.233	0.035	1.268
filterfun_sample	0.020	0.000	0.021
gapstat_ord	2.262	0.045	2.309
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0	0	0
get_sample-methods	0.005	0.004	0.008
get_taxa-methods	0.003	0.003	0.006
get_taxa_unique	0.260	0.025	0.285
get_variable	0.221	0.010	0.231
getslots.phyloseq	0.224	0.016	0.240
import	0.001	0.000	0.001
import_RDP_otu	0.759	0.027	0.786
import_biom	0.182	0.002	0.205
import_env_file	0.001	0.000	0.001
import_mothur	0.001	0.000	0.002
import_mothur_dist	0.001	0.000	0.001
import_pyrotagger_tab	0.001	0.000	0.000
import_qiime	0.637	0.009	0.646
import_qiime_otu_tax	0.549	0.047	0.596
import_qiime_sample_data	0.019	0.001	0.019
import_usearch_uc	0.012	0.003	0.015
index_reorder	0	0	0
intersect_taxa	0.001	0.000	0.001
make_network	3.388	0.081	3.474
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.970	0.175	1.146
merge_taxa-methods	0.064	0.002	0.066
microbio_me_qiime	0.653	0.024	0.708
mt-methods	1.472	0.023	1.498
nodeplotblank	0.260	0.006	0.267
nodeplotboot	0.001	0.000	0.001
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.026	0.004	0.030
ntaxa-methods	0.004	0.006	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	0.200	0.015	0.215
phyloseq	0.029	0.007	0.036
phyloseq_to_deseq2	2.294	0.090	2.385
phyloseq_to_metagenomeSeq	1.895	0.101	1.996
plot_bar	2.125	0.130	2.260
plot_clusgap	3.590	0.181	3.800
plot_heatmap	4.472	0.272	4.854
plot_net	4.554	0.140	4.725
plot_network	2.617	0.034	2.658
plot_ordination	0.632	0.060	0.693
plot_phyloseq-methods	0.265	0.003	0.267
plot_richness	4.558	0.468	5.047
plot_scree	1.916	0.083	2.012
plot_tree	0.773	0.009	0.782
prune_samples-methods	0.641	0.109	0.752
prune_taxa-methods	0.044	0.005	0.050
psmelt	0.954	0.108	1.063
rank_names	0.026	0.005	0.031
rarefy_even_depth	0.125	0.007	0.131
read_tree	0.158	0.001	0.159
read_tree_greengenes	0.047	0.001	0.048
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.211	0.014	0.225
rm_outlierf	0.023	0.001	0.023
sample_data-methods	0.050	0.007	0.058
sample_names-methods	0.003	0.005	0.008
sample_sums	0.031	0.014	0.045
sample_variables	0.025	0.006	0.032
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0.001	0.000	0.000
subset_ord_plot	0.001	0.000	0.001
subset_samples-methods	0.001	0.000	0.000
subset_taxa-methods	0	0	0
tax_glom	0.001	0.000	0.001
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.035	0.007	0.041
taxa_sums	0.040	0.016	0.055
threshrank	2.441	0.864	3.311
threshrankfun	0.048	0.002	0.050
tip_glom	0.783	0.006	0.789
topf	0.021	0.000	0.021
topk	0.020	0.001	0.020
topp	0.020	0.001	0.020
transformcounts	0.141	0.003	0.144
transpose-methods	0.822	0.528	1.350
tree_layout	0.569	0.007	0.608