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: 2015-10-27 10:55:53 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:02:20 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 387.5 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 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 ... [87s/89s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 6.494  0.507   7.003
plot_net      5.230  0.126   5.365
plot_heatmap  4.821  0.282   5.106
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [89s/90s]
 [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	4.377	0.200	4.601
JSD	0.001	0.000	0.001
UniFrac-methods	0.146	0.016	0.162
access	0.000	0.000	0.001
assign-otu_table	0.001	0.001	0.001
assign-phy_tree	0.052	0.014	0.066
assign-sample_data	0.142	0.035	0.177
assign-sample_names	0.009	0.002	0.011
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.003	0.002	0.004
assign-taxa_names	0.009	0.003	0.012
build_tax_table	0.016	0.000	0.016
capscale-phyloseq-methods	0.903	0.078	1.063
cca-rda-phyloseq-methods	0.001	0.000	0.001
chunkReOrder	0.001	0.000	0.001
data-GlobalPatterns	1.986	0.071	2.057
data-enterotype	1.962	0.021	1.983
data-esophagus	0.771	0.008	0.780
data-soilrep	1.950	0.154	2.105
distance	0.216	0.042	1.464
distanceMethodList	0.001	0.001	0.001
envHash2otu_table	0.001	0.000	0.000
estimate_richness	0.029	0.004	0.033
export_env_file	0.001	0.000	0.001
export_mothur_dist	0.115	0.021	0.135
extract-methods	0.010	0.004	0.014
filter_taxa	1.258	0.042	1.300
filterfun_sample	0.022	0.000	0.023
gapstat_ord	2.519	0.095	2.615
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.001	0.000	0.001
get_sample-methods	0.004	0.007	0.011
get_taxa-methods	0.004	0.007	0.010
get_taxa_unique	0.275	0.033	0.309
get_variable	0.206	0.013	0.220
getslots.phyloseq	0.214	0.026	0.241
import	0	0	0
import_RDP_otu	1.306	0.036	1.341
import_biom	0.212	0.013	0.233
import_env_file	0	0	0
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.001	0.000	0.001
import_pyrotagger_tab	0	0	0
import_qiime	0.809	0.003	0.812
import_qiime_otu_tax	0.737	0.054	0.791
import_qiime_sample_data	0.021	0.001	0.023
import_usearch_uc	0.018	0.004	0.022
index_reorder	0.001	0.000	0.001
intersect_taxa	0.001	0.000	0.000
make_network	3.672	0.093	3.766
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.002	0.001	0.001
merge_samples-methods	1.500	0.221	1.721
merge_taxa-methods	0.071	0.003	0.073
microbio_me_qiime	0.642	0.042	0.908
mt-methods	2.296	0.029	2.325
nodeplotblank	0.390	0.004	0.403
nodeplotboot	0.003	0.000	0.002
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.032	0.002	0.033
ntaxa-methods	0.005	0.002	0.006
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	0.217	0.016	0.232
phyloseq	0.032	0.006	0.038
phyloseq_to_deseq2	2.995	0.118	3.114
phyloseq_to_metagenomeSeq	1.506	0.119	1.625
plot_bar	2.802	0.180	2.983
plot_clusgap	4.399	0.185	4.610
plot_heatmap	4.821	0.282	5.106
plot_net	5.230	0.126	5.365
plot_network	2.909	0.039	2.951
plot_ordination	0.869	0.073	0.942
plot_phyloseq-methods	0.275	0.002	0.278
plot_richness	6.494	0.507	7.003
plot_scree	1.845	0.077	1.924
plot_tree	0.707	0.005	0.713
prune_samples-methods	0.718	0.124	0.884
prune_taxa-methods	0.040	0.004	0.045
psmelt	1.064	0.131	1.195
rank_names	0.029	0.007	0.035
rarefy_even_depth	0.109	0.004	0.113
read_tree	0.151	0.002	0.153
read_tree_greengenes	0.048	0.001	0.049
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.215	0.016	0.231
rm_outlierf	0.023	0.001	0.023
sample_data-methods	0.076	0.012	0.088
sample_names-methods	0.003	0.007	0.010
sample_sums	0.035	0.016	0.052
sample_variables	0.031	0.009	0.039
show-methods	0.001	0.000	0.001
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0	0	0
subset_samples-methods	0.001	0.000	0.000
subset_taxa-methods	0.001	0.000	0.000
tax_glom	0.001	0.000	0.001
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.032	0.007	0.039
taxa_sums	0.042	0.020	0.062
threshrank	3.156	1.143	4.312
threshrankfun	0.071	0.003	0.073
tip_glom	0.883	0.007	0.891
topf	0.018	0.000	0.019
topk	0.017	0.000	0.018
topp	0.018	0.001	0.018
transformcounts	0.132	0.003	0.135
transpose-methods	1.525	0.667	2.578
tree_layout	0.698	0.009	0.725