BioC 3.3: CHECK report for phyloseq on linux2.bioconductor.org

Package: phyloseq

Version: 1.15.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.15.0.tar.gz

StartedAt: 2015-10-27 06:43:37 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:47:49 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 251.9 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/phyloseq.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.15.0’
* 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 ... [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’
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 ... [61s/61s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [62s/62s]
 [62s/62s] 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-3.3-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	3.062	0.000	3.062
JSD	0.001	0.000	0.001
UniFrac-methods	0.162	0.000	0.162
access	0.000	0.000	0.001
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.046	0.007	0.053
assign-sample_data	0.815	0.008	0.822
assign-sample_names	0.009	0.000	0.009
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.003	0.000	0.003
assign-taxa_names	0.008	0.000	0.008
build_tax_table	0.014	0.000	0.014
capscale-phyloseq-methods	0.841	0.004	0.844
cca-rda-phyloseq-methods	0.001	0.000	0.000
chunkReOrder	0.001	0.000	0.001
data-GlobalPatterns	1.624	0.012	1.637
data-enterotype	2.088	0.008	2.096
data-esophagus	0.809	0.000	0.808
data-soilrep	1.465	0.020	1.485
distance	0.163	0.017	0.190
distanceMethodList	0.001	0.000	0.001
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.030	0.004	0.034
export_env_file	0.001	0.000	0.000
export_mothur_dist	0.112	0.007	0.121
extract-methods	0.01	0.00	0.01
filter_taxa	1.090	0.015	1.107
filterfun_sample	0.021	0.000	0.021
gapstat_ord	2.216	0.024	2.241
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0	0	0
get_sample-methods	0.002	0.003	0.004
get_taxa-methods	0.003	0.000	0.004
get_taxa_unique	0.319	0.000	0.319
get_variable	0.255	0.000	0.255
getslots.phyloseq	0.261	0.004	0.265
import	0	0	0
import_RDP_otu	1.072	0.000	1.072
import_biom	0.178	0.000	0.178
import_env_file	0.001	0.000	0.001
import_mothur	0.001	0.000	0.001
import_mothur_dist	0	0	0
import_pyrotagger_tab	0	0	0
import_qiime	0.762	0.000	0.762
import_qiime_otu_tax	0.642	0.031	0.674
import_qiime_sample_data	0.020	0.001	0.020
import_usearch_uc	0.011	0.007	0.019
index_reorder	0.000	0.000	0.001
intersect_taxa	0.000	0.000	0.001
make_network	3.105	0.016	3.121
merge_phyloseq	0	0	0
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.587	0.016	0.603
merge_taxa-methods	0.042	0.000	0.043
microbio_me_qiime	0.420	0.048	0.469
mt-methods	1.204	0.008	1.212
nodeplotblank	0.240	0.004	0.244
nodeplotboot	0.001	0.000	0.002
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.019	0.000	0.019
ntaxa-methods	0.003	0.000	0.002
ordinate	0.001	0.000	0.000
otu_table-methods	0.001	0.000	0.000
parseTaxonomy-functions	0.001	0.000	0.002
phy_tree-methods	0.161	0.004	0.165
phyloseq	0.019	0.000	0.019
phyloseq_to_deseq2	2.159	0.099	2.255
phyloseq_to_metagenomeSeq	1.184	0.003	1.188
plot_bar	2.138	0.025	2.162
plot_clusgap	2.905	0.028	2.933
plot_heatmap	2.866	0.004	2.871
plot_net	3.305	0.008	3.316
plot_network	1.938	0.003	1.945
plot_ordination	0.506	0.004	0.511
plot_phyloseq-methods	0.199	0.000	0.200
plot_richness	3.938	0.008	3.950
plot_scree	1.915	0.004	1.927
plot_tree	0.725	0.008	0.734
prune_samples-methods	0.523	0.004	0.528
prune_taxa-methods	0.025	0.000	0.025
psmelt	1.211	0.004	1.216
rank_names	0.031	0.000	0.031
rarefy_even_depth	0.115	0.000	0.115
read_tree	0.157	0.004	0.161
read_tree_greengenes	0.030	0.000	0.029
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.135	0.004	0.139
rm_outlierf	0.017	0.000	0.017
sample_data-methods	0.045	0.000	0.045
sample_names-methods	0.002	0.000	0.003
sample_sums	0.021	0.004	0.025
sample_variables	0.017	0.004	0.022
show-methods	0	0	0
splat.phyloseq.objects	0.001	0.000	0.000
subset_ord_plot	0.001	0.000	0.000
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.000	0.000	0.001
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.024	0.000	0.024
taxa_sums	0.029	0.000	0.029
threshrank	1.807	0.392	2.198
threshrankfun	0.045	0.000	0.046
tip_glom	0.602	0.004	0.606
topf	0.011	0.000	0.012
topk	0.011	0.000	0.011
topp	0.007	0.000	0.011
transformcounts	0.08	0.00	0.08
transpose-methods	0.558	0.256	0.814
tree_layout	0.376	0.000	0.376