BioC 3.0: CHECK report for phyloseq on zin1

Package: phyloseq

Version: 1.10.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.10.0.tar.gz

StartedAt: 2015-04-10 02:58:13 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:06:09 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 476.3 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/phyloseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.10.0’
* 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 ... [28s/29s] 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘JSD.pair’
* 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
JSD: no visible binding for global variable ‘i’
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’
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 ... [82s/92s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_net      6.664  0.004   7.205
plot_clusgap  5.325  0.028   5.612
plot_richness 5.228  0.020   5.255
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [86s/90s]
 [86s/91s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-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 ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: 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 ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’: not turning on duplicate class definitions for this class.
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.365	0.016	3.730
JSD	0.004	0.000	0.001
UniFrac-methods	0.144	0.024	0.230
access	0.004	0.000	0.001
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.040	0.000	0.049
assign-sample_data	0.764	0.020	0.817
assign-sample_names	0.008	0.000	0.009
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.004	0.000	0.002
assign-taxa_names	0.008	0.000	0.007
build_tax_table	0.012	0.000	0.013
capscale-phyloseq-methods	1.256	0.000	1.283
cca-rda-phyloseq-methods	0.000	0.000	0.001
data-GlobalPatterns	2.008	0.016	2.238
data-enterotype	2.564	0.004	2.571
data-esophagus	0.776	0.000	0.776
data-soilrep	1.540	0.016	1.558
distance	0.340	0.056	2.550
envHash2otu_table	0.000	0.000	0.001
estimate_richness	0.028	0.000	0.026
export_env_file	0	0	0
export_mothur_dist	0.044	0.028	0.071
extract-methods	0.012	0.000	0.011
filter_taxa	0.532	0.028	0.563
filterfun_sample	0.02	0.00	0.02
gapstat_ord	2.188	0.016	3.711
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0.004	0.000	0.000
get_sample-methods	0.004	0.000	0.004
get_taxa-methods	0.000	0.004	0.003
get_taxa_unique	0.208	0.016	0.226
get_variable	0.168	0.004	0.173
getslots.phyloseq	0.168	0.004	0.176
import	0.000	0.000	0.001
import_RDP_otu	1.008	0.008	1.102
import_biom	0.516	0.000	0.521
import_env_file	0.000	0.000	0.001
import_mothur	0.004	0.000	0.001
import_mothur_dist	0.000	0.000	0.001
import_pyrotagger_tab	0	0	0
import_qiime	0.584	0.004	0.769
import_qiime_otu_tax	0.516	0.016	0.764
import_qiime_sample_data	0.024	0.000	0.026
import_usearch_uc	0.02	0.00	0.02
index_reorder	0.000	0.000	0.001
intersect_taxa	0.004	0.000	0.001
make_network	4.013	0.012	4.103
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	1.416	0.008	1.476
merge_taxa-methods	0.060	0.000	0.059
microbio_me_qiime	0.624	0.064	0.733
mt-methods	1.632	0.004	1.720
nodeplotblank	0.380	0.000	0.382
nodeplotboot	0.000	0.000	0.002
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.020	0.000	0.021
ntaxa-methods	0.004	0.000	0.003
ordinate	0.000	0.000	0.001
otu_table-methods	0.000	0.000	0.001
parseTaxonomy-functions	0.000	0.000	0.002
phy_tree-methods	0.184	0.012	0.286
phyloseq	0.028	0.000	0.027
phyloseq_to_deseq2	0.788	0.028	0.817
plot_bar	2.624	0.012	2.640
plot_clusgap	5.325	0.028	5.612
plot_heatmap	4.372	0.052	4.432
plot_net	6.664	0.004	7.205
plot_network	3.192	0.008	3.278
plot_ordination	0.872	0.008	0.882
plot_phyloseq-methods	0.277	0.000	0.277
plot_richness	5.228	0.020	5.255
plot_scree	1.776	0.004	1.785
plot_tree	0.760	0.000	0.759
prune_samples-methods	0.740	0.004	0.746
prune_taxa-methods	0.028	0.000	0.032
psmelt	1.320	0.012	1.334
rank_names	0.024	0.000	0.025
rarefy_even_depth	0.072	0.000	0.074
read_tree	0.136	0.000	0.134
read_tree_greengenes	0.044	0.000	0.116
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.184	0.008	0.228
rm_outlierf	0.016	0.000	0.018
sample_data-methods	0.048	0.000	0.052
sample_names-methods	0.004	0.000	0.003
sample_sums	0.032	0.000	0.030
sample_variables	0.024	0.000	0.025
show-methods	0.000	0.000	0.001
splat.phyloseq.objects	0	0	0
subset_ord_plot	0.000	0.000	0.001
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.004	0.000	0.000
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.02	0.00	0.02
taxa_sums	0.032	0.000	0.035
threshrank	2.664	0.592	3.445
threshrankfun	0.052	0.000	0.053
tip_glom	0.820	0.004	0.827
topf	0.016	0.000	0.019
topk	0.024	0.000	0.024
topp	0.016	0.000	0.018
transformcounts	0.104	0.000	0.103
transpose-methods	0.732	0.320	1.055
tree_layout	0.636	0.004	3.619