BioC 3.2: CHECK report for phyloseq on perceval

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: 2015-11-10 08:04:48 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:11:11 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 383.1 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.14.0’
* 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 ... [19s/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 ... [86s/87s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 5.615  0.528   6.154
plot_net      5.105  0.140   5.254
plot_heatmap  4.732  0.267   5.004
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [89s/89s]
 [90s/90s] 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	4.373	0.190	4.579
JSD	0.001	0.000	0.001
UniFrac-methods	0.145	0.013	0.159
access	0.000	0.000	0.001
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.054	0.013	0.067
assign-sample_data	0.142	0.029	0.171
assign-sample_names	0.011	0.007	0.017
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.003	0.007	0.011
assign-taxa_names	0.010	0.007	0.018
build_tax_table	0.017	0.001	0.018
capscale-phyloseq-methods	0.898	0.080	0.977
cca-rda-phyloseq-methods	0.001	0.000	0.001
chunkReOrder	0.001	0.000	0.001
data-GlobalPatterns	1.932	0.067	1.999
data-enterotype	1.915	0.019	1.934
data-esophagus	0.756	0.006	0.763
data-soilrep	1.893	0.145	2.039
distance	0.206	0.031	1.059
distanceMethodList	0.001	0.001	0.001
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.030	0.003	0.034
export_env_file	0.000	0.001	0.001
export_mothur_dist	0.116	0.020	0.137
extract-methods	0.010	0.003	0.014
filter_taxa	1.292	0.042	1.333
filterfun_sample	0.023	0.001	0.023
gapstat_ord	2.512	0.060	2.572
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0	0	0
get_sample-methods	0.004	0.004	0.008
get_taxa-methods	0.004	0.004	0.008
get_taxa_unique	0.273	0.027	0.299
get_variable	0.208	0.012	0.220
getslots.phyloseq	0.212	0.023	0.234
import	0.001	0.000	0.000
import_RDP_otu	1.284	0.039	1.322
import_biom	0.224	0.034	0.275
import_env_file	0.001	0.000	0.000
import_mothur	0.001	0.000	0.001
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.802	0.005	0.808
import_qiime_otu_tax	0.697	0.052	0.749
import_qiime_sample_data	0.022	0.001	0.022
import_usearch_uc	0.018	0.004	0.022
index_reorder	0.001	0.000	0.001
intersect_taxa	0.000	0.000	0.001
make_network	3.679	0.093	3.774
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.001	0.001
merge_samples-methods	1.503	0.226	1.729
merge_taxa-methods	0.071	0.002	0.073
microbio_me_qiime	0.643	0.027	0.772
mt-methods	2.185	0.029	2.214
nodeplotblank	0.409	0.009	0.419
nodeplotboot	0.003	0.000	0.003
nodeplotdefault	0.001	0.001	0.001
nsamples-methods	0.033	0.003	0.035
ntaxa-methods	0.005	0.003	0.007
ordinate	0.001	0.000	0.000
otu_table-methods	0.001	0.000	0.000
parseTaxonomy-functions	0.004	0.000	0.004
phy_tree-methods	0.216	0.016	0.232
phyloseq	0.029	0.006	0.035
phyloseq_to_deseq2	2.862	0.095	2.958
phyloseq_to_metagenomeSeq	1.959	0.132	2.091
plot_bar	2.708	0.185	2.894
plot_clusgap	4.707	0.178	4.908
plot_heatmap	4.732	0.267	5.004
plot_net	5.105	0.140	5.254
plot_network	2.854	0.036	2.892
plot_ordination	0.869	0.079	0.949
plot_phyloseq-methods	0.278	0.004	0.283
plot_richness	5.615	0.528	6.154
plot_scree	1.935	0.086	2.024
plot_tree	0.702	0.009	0.713
prune_samples-methods	1.194	0.128	1.322
prune_taxa-methods	0.043	0.008	0.050
psmelt	1.045	0.136	1.182
rank_names	0.029	0.006	0.035
rarefy_even_depth	0.107	0.003	0.110
read_tree	0.157	0.004	0.161
read_tree_greengenes	0.050	0.001	0.050
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.215	0.019	0.233
rm_outlierf	0.024	0.001	0.025
sample_data-methods	0.067	0.012	0.080
sample_names-methods	0.003	0.009	0.013
sample_sums	0.035	0.021	0.057
sample_variables	0.029	0.011	0.040
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0.001	0.000	0.001
subset_ord_plot	0.001	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	0.000
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.033	0.010	0.044
taxa_sums	0.042	0.024	0.066
threshrank	3.182	1.148	4.332
threshrankfun	0.070	0.005	0.075
tip_glom	0.893	0.010	0.904
topf	0.019	0.001	0.019
topk	0.018	0.000	0.018
topp	0.019	0.000	0.019
transformcounts	0.128	0.006	0.134
transpose-methods	1.014	0.656	1.671
tree_layout	0.633	0.012	0.654