BioC 3.2: CHECK report for phyloseq on zin1

Package: phyloseq

Version: 1.13.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.13.2.tar.gz

StartedAt: 2015-08-24 02:32:16 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:37:45 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 329.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: phyloseq.Rcheck

Warnings: 1

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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_1.13.2.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 ‘1.13.2’
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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 ... WARNING
Undocumented S4 classes:
  ‘dist’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 1 WARNING, 4 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	3.370	0.028	3.412
JSD	0.001	0.000	0.000
UniFrac-methods	0.101	0.000	0.105
access	0.001	0.000	0.001
assign-otu_table	0.000	0.000	0.001
assign-phy_tree	0.037	0.000	0.037
assign-sample_data	0.464	0.012	0.475
assign-sample_names	0.008	0.000	0.008
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.003	0.000	0.003
assign-taxa_names	0.007	0.000	0.008
build_tax_table	0.013	0.000	0.013
capscale-phyloseq-methods	0.991	0.004	0.994
cca-rda-phyloseq-methods	0.000	0.000	0.001
data-GlobalPatterns	1.444	0.000	1.445
data-enterotype	1.969	0.008	1.975
data-esophagus	0.56	0.00	0.56
data-soilrep	1.377	0.008	1.384
distance	0.161	0.038	0.405
envHash2otu_table	0.001	0.000	0.000
estimate_richness	0.028	0.000	0.028
export_env_file	0.000	0.000	0.001
export_mothur_dist	0.080	0.020	0.101
extract-methods	0.008	0.000	0.009
filter_taxa	0.163	0.004	0.167
filterfun_sample	0.017	0.000	0.018
gapstat_ord	1.783	0.052	1.833
genefilter_sample-methods	0.000	0.000	0.001
get.component.classes	0	0	0
get_sample-methods	0.003	0.000	0.003
get_taxa-methods	0.003	0.000	0.003
get_taxa_unique	0.194	0.012	0.206
get_variable	0.155	0.004	0.160
getslots.phyloseq	0.159	0.004	0.163
import	0.001	0.000	0.000
import_RDP_otu	0.512	0.000	0.513
import_biom	0.164	0.004	0.167
import_env_file	0	0	0
import_mothur	0.001	0.000	0.001
import_mothur_dist	0	0	0
import_pyrotagger_tab	0.001	0.000	0.001
import_qiime	0.663	0.004	0.666
import_qiime_otu_tax	0.56	0.02	0.58
import_qiime_sample_data	0.018	0.000	0.018
import_usearch_uc	0.010	0.004	0.014
index_reorder	0.001	0.000	0.000
intersect_taxa	0	0	0
make_network	3.052	0.023	3.079
merge_phyloseq	0.001	0.000	0.000
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	1.264	0.008	1.273
merge_taxa-methods	0.059	0.000	0.059
microbio_me_qiime	0.606	0.057	0.665
mt-methods	1.465	0.008	1.472
nodeplotblank	0.307	0.000	0.307
nodeplotboot	0.002	0.001	0.001
nodeplotdefault	0	0	0
nsamples-methods	0.020	0.003	0.025
ntaxa-methods	0.003	0.000	0.004
ordinate	0.001	0.000	0.001
otu_table-methods	0	0	0
parseTaxonomy-functions	0.003	0.000	0.002
phy_tree-methods	0.172	0.008	0.179
phyloseq	0.023	0.000	0.023
phyloseq_to_deseq2	1.181	0.031	1.224
plot_bar	2.141	0.000	2.145
plot_clusgap	3.925	0.024	3.966
plot_heatmap	3.583	0.004	3.591
plot_net	4.570	0.004	4.579
plot_network	2.771	0.004	2.779
plot_ordination	0.671	0.000	0.671
plot_phyloseq-methods	0.204	0.000	0.204
plot_richness	3.793	0.004	3.826
plot_scree	1.451	0.004	1.457
plot_tree	0.910	0.000	0.911
prune_samples-methods	0.524	0.004	0.528
prune_taxa-methods	0.031	0.000	0.032
psmelt	0.771	0.008	0.779
rank_names	0.020	0.004	0.024
rarefy_even_depth	0.085	0.000	0.085
read_tree	0.109	0.000	0.110
read_tree_greengenes	0.045	0.004	0.049
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.155	0.000	0.154
rm_outlierf	0.013	0.000	0.014
sample_data-methods	0.039	0.000	0.043
sample_names-methods	0.003	0.000	0.002
sample_sums	0.023	0.004	0.028
sample_variables	0.024	0.000	0.023
show-methods	0.000	0.000	0.001
splat.phyloseq.objects	0	0	0
subset_ord_plot	0.001	0.000	0.000
subset_samples-methods	0.000	0.000	0.001
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.001	0.000	0.000
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.023	0.000	0.024
taxa_sums	0.033	0.000	0.033
threshrank	2.295	0.483	2.807
threshrankfun	0.051	0.000	0.051
tip_glom	0.690	0.000	0.703
topf	0.015	0.000	0.016
topk	0.014	0.000	0.014
topp	0.015	0.000	0.015
transformcounts	0.106	0.000	0.106
transpose-methods	1.041	0.356	1.395
tree_layout	0.549	0.000	0.549