BioC 3.3: CHECK report for phyloseq on morelia

Package: phyloseq

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.15.0.tar.gz

StartedAt: 2015-10-22 09:34:03 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 09:38:20 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 257.4 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 phyloseq_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.15.0’
* 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 ... [14s/15s] 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’
Undefined global functions or variables:
  #OTU ID .SD := Abundance Consensus Lineage J OTU SE.sim Sample V1 V2
  X0 eigenvalue esophagus gap h.adj.index i k label read se value
  vertex vmax vmin x xdodge xend xfartiplab xleft xright y yend
* 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 ... [55s/57s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [60s/60s]
 [60s/60s] 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-3.3-bioc/meat/phyloseq.Rcheck/00check.log’
for details.

* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	2.184	0.135	2.391
JSD	0.001	0.000	0.000
UniFrac-methods	0.089	0.009	0.098
access	0.000	0.000	0.001
assign-otu_table	0.000	0.001	0.000
assign-phy_tree	0.044	0.002	0.046
assign-sample_data	0.464	0.016	0.480
assign-sample_names	0.005	0.002	0.007
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.002	0.001	0.003
assign-taxa_names	0.005	0.001	0.006
build_tax_table	0.009	0.001	0.010
capscale-phyloseq-methods	0.522	0.032	0.554
cca-rda-phyloseq-methods	0.000	0.000	0.001
chunkReOrder	0.001	0.000	0.000
data-GlobalPatterns	0.905	0.040	0.945
data-enterotype	1.138	0.028	1.167
data-esophagus	0.441	0.004	0.445
data-soilrep	1.123	0.096	1.219
distance	0.138	0.026	1.349
distanceMethodList	0.001	0.000	0.001
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.018	0.001	0.019
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.067	0.011	0.077
extract-methods	0.006	0.001	0.007
filter_taxa	0.637	0.018	0.654
filterfun_sample	0.013	0.000	0.014
gapstat_ord	1.534	0.038	1.583
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0.001	0.000	0.000
get_sample-methods	0.003	0.002	0.004
get_taxa-methods	0.003	0.002	0.005
get_taxa_unique	0.189	0.015	0.203
get_variable	0.151	0.005	0.157
getslots.phyloseq	0.183	0.012	0.195
import	0.000	0.000	0.001
import_RDP_otu	0.872	0.028	0.900
import_biom	0.132	0.001	0.251
import_env_file	0	0	0
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.000	0.001	0.000
import_pyrotagger_tab	0	0	0
import_qiime	0.539	0.005	0.544
import_qiime_otu_tax	0.473	0.032	0.507
import_qiime_sample_data	0.014	0.001	0.015
import_usearch_uc	0.011	0.002	0.014
index_reorder	0.000	0.001	0.000
intersect_taxa	0.000	0.000	0.001
make_network	2.289	0.065	2.354
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.000
merge_samples-methods	0.640	0.125	0.764
merge_taxa-methods	0.057	0.005	0.063
microbio_me_qiime	0.508	0.018	0.555
mt-methods	1.029	0.018	1.047
nodeplotblank	0.343	0.010	0.354
nodeplotboot	0.002	0.000	0.002
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.021	0.006	0.027
ntaxa-methods	0.003	0.004	0.007
ordinate	0	0	0
otu_table-methods	0.001	0.000	0.000
parseTaxonomy-functions	0.002	0.000	0.002
phy_tree-methods	0.164	0.020	0.184
phyloseq	0.019	0.007	0.026
phyloseq_to_deseq2	2.389	0.083	2.474
phyloseq_to_metagenomeSeq	1.200	0.069	1.270
plot_bar	2.123	0.084	2.209
plot_clusgap	3.284	0.116	3.426
plot_heatmap	3.393	0.196	3.655
plot_net	3.559	0.100	3.671
plot_network	2.491	0.031	2.527
plot_ordination	0.599	0.056	0.656
plot_phyloseq-methods	0.178	0.002	0.179
plot_richness	3.653	0.334	4.114
plot_scree	1.709	0.071	1.782
plot_tree	0.590	0.005	0.596
prune_samples-methods	0.351	0.060	0.412
prune_taxa-methods	0.025	0.004	0.029
psmelt	0.562	0.071	0.633
rank_names	0.020	0.003	0.023
rarefy_even_depth	0.067	0.002	0.070
read_tree	0.088	0.001	0.089
read_tree_greengenes	0.037	0.001	0.038
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.137	0.007	0.144
rm_outlierf	0.016	0.001	0.015
sample_data-methods	0.044	0.005	0.049
sample_names-methods	0.002	0.004	0.006
sample_sums	0.025	0.010	0.034
sample_variables	0.021	0.004	0.026
show-methods	0.001	0.000	0.000
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.001	0.000	0.000
tax_table-methods	0.000	0.001	0.001
taxa_names-methods	0.021	0.004	0.025
taxa_sums	0.029	0.010	0.039
threshrank	1.883	0.652	2.535
threshrankfun	0.050	0.003	0.053
tip_glom	0.557	0.008	0.565
topf	0.012	0.000	0.012
topk	0.011	0.000	0.011
topp	0.011	0.000	0.011
transformcounts	0.082	0.003	0.084
transpose-methods	0.896	0.394	1.292
tree_layout	0.446	0.005	0.478