BioC 3.2: CHECK report for phyloseq on linux1.bioconductor.org

Package: phyloseq

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.14.0.tar.gz

StartedAt: 2015-10-27 06:41:53 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:46:34 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 281.3 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [13s/13s] 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 ... [64s/64s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [70s/70s]
 [70s/70s] 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
  ‘/home/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	2.848	0.048	2.900
JSD	0	0	0
UniFrac-methods	0.104	0.004	0.108
access	0	0	0
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.034	0.000	0.035
assign-sample_data	0.362	0.000	0.362
assign-sample_names	0.006	0.004	0.006
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.001	0.000	0.002
assign-taxa_names	0.006	0.000	0.006
build_tax_table	0.011	0.000	0.010
capscale-phyloseq-methods	0.605	0.004	0.609
cca-rda-phyloseq-methods	0.000	0.000	0.001
chunkReOrder	0.001	0.000	0.001
data-GlobalPatterns	1.663	0.016	1.685
data-enterotype	1.340	0.000	1.345
data-esophagus	0.785	0.004	0.789
data-soilrep	1.739	0.008	1.747
distance	0.131	0.015	0.155
distanceMethodList	0.001	0.000	0.000
envHash2otu_table	0	0	0
estimate_richness	0.022	0.000	0.022
export_env_file	0	0	0
export_mothur_dist	0.062	0.016	0.078
extract-methods	0.008	0.000	0.007
filter_taxa	0.795	0.016	0.811
filterfun_sample	0.013	0.000	0.014
gapstat_ord	1.557	0.032	1.589
genefilter_sample-methods	0.001	0.000	0.000
get.component.classes	0	0	0
get_sample-methods	0.002	0.000	0.003
get_taxa-methods	0.003	0.000	0.003
get_taxa_unique	0.184	0.000	0.184
get_variable	0.145	0.000	0.146
getslots.phyloseq	0.151	0.000	0.151
import	0.000	0.000	0.001
import_RDP_otu	0.809	0.000	0.810
import_biom	0.118	0.000	0.118
import_env_file	0	0	0
import_mothur	0.000	0.000	0.001
import_mothur_dist	0.001	0.000	0.000
import_pyrotagger_tab	0.001	0.000	0.000
import_qiime	0.558	0.000	0.558
import_qiime_otu_tax	0.474	0.036	0.510
import_qiime_sample_data	0.012	0.000	0.012
import_usearch_uc	0.011	0.000	0.012
index_reorder	0.000	0.000	0.001
intersect_taxa	0.001	0.000	0.001
make_network	3.302	0.016	3.327
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	1.001	0.012	1.021
merge_taxa-methods	0.045	0.000	0.045
microbio_me_qiime	0.451	0.047	0.498
mt-methods	1.489	0.000	1.492
nodeplotblank	0.23	0.00	0.23
nodeplotboot	0.001	0.000	0.001
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.020	0.000	0.021
ntaxa-methods	0.003	0.000	0.002
ordinate	0.000	0.000	0.001
otu_table-methods	0.000	0.000	0.001
parseTaxonomy-functions	0.002	0.000	0.002
phy_tree-methods	0.147	0.000	0.147
phyloseq	0.015	0.004	0.019
phyloseq_to_deseq2	3.415	0.126	3.538
phyloseq_to_metagenomeSeq	1.326	0.036	1.363
plot_bar	1.799	0.008	1.808
plot_clusgap	4.165	0.028	4.201
plot_heatmap	3.163	0.020	3.190
plot_net	4.505	0.008	4.515
plot_network	2.853	0.004	2.858
plot_ordination	0.952	0.008	0.963
plot_phyloseq-methods	0.269	0.000	0.269
plot_richness	3.961	0.028	3.989
plot_scree	1.537	0.000	1.541
plot_tree	0.571	0.000	0.571
prune_samples-methods	0.513	0.004	0.519
prune_taxa-methods	0.025	0.000	0.026
psmelt	0.833	0.004	0.840
rank_names	0.028	0.004	0.031
rarefy_even_depth	0.121	0.000	0.121
read_tree	0.166	0.004	0.170
read_tree_greengenes	0.055	0.000	0.055
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.250	0.000	0.249
rm_outlierf	0.025	0.000	0.025
sample_data-methods	0.067	0.000	0.067
sample_names-methods	0.000	0.000	0.003
sample_sums	0.035	0.000	0.035
sample_variables	0.032	0.000	0.031
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	0.000	0.000	0.001
subset_taxa-methods	0	0	0
tax_glom	0.000	0.000	0.001
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.035	0.004	0.039
taxa_sums	0.036	0.004	0.043
threshrank	2.808	0.503	3.320
threshrankfun	0.073	0.000	0.073
tip_glom	1.261	0.000	1.263
topf	0.012	0.000	0.013
topk	0.011	0.000	0.011
topp	0.011	0.000	0.011
transformcounts	0.086	0.000	0.086
transpose-methods	0.568	0.356	0.929
tree_layout	0.481	0.000	0.482