BioC 3.2: CHECK report for phyloseq on oaxaca

Package: phyloseq

Version: 1.13.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.13.2.tar.gz

StartedAt: 2015-08-24 02:37:52 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:45:39 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 467.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: phyloseq.Rcheck

Warnings: 1

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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_1.13.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/phyloseq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.13.2’
* 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 ... [26s/27s] 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 ... [85s/87s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 5.255  0.514   5.785
plot_net      5.330  0.161   5.599
plot_heatmap  4.972  0.220   5.367
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [96s/98s]
 [96s/99s] 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
  ‘/Users/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	4.269	0.176	4.500
JSD	0.001	0.000	0.001
UniFrac-methods	0.152	0.004	0.155
access	0.000	0.000	0.001
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.052	0.005	0.058
assign-sample_data	0.480	0.022	0.504
assign-sample_names	0.011	0.001	0.012
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.004	0.002	0.005
assign-taxa_names	0.010	0.002	0.012
build_tax_table	0.019	0.001	0.020
capscale-phyloseq-methods	1.263	0.079	1.345
cca-rda-phyloseq-methods	0.001	0.000	0.001
data-GlobalPatterns	1.371	0.075	1.485
data-enterotype	2.449	0.049	2.556
data-esophagus	0.829	0.008	0.838
data-soilrep	1.865	0.151	2.046
distance	0.278	0.043	1.838
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.033	0.003	0.035
export_env_file	0.001	0.000	0.000
export_mothur_dist	0.105	0.018	0.123
extract-methods	0.013	0.002	0.014
filter_taxa	0.630	0.051	0.681
filterfun_sample	0.025	0.000	0.026
gapstat_ord	2.303	0.051	2.408
genefilter_sample-methods	0.000	0.001	0.001
get.component.classes	0.000	0.000	0.001
get_sample-methods	0.004	0.002	0.007
get_taxa-methods	0.004	0.003	0.007
get_taxa_unique	0.297	0.023	0.329
get_variable	0.225	0.007	0.241
getslots.phyloseq	0.264	0.025	0.290
import	0	0	0
import_RDP_otu	1.287	0.019	1.308
import_biom	0.213	0.004	0.249
import_env_file	0.000	0.000	0.001
import_mothur	0.001	0.000	0.001
import_mothur_dist	0.001	0.000	0.001
import_pyrotagger_tab	0.001	0.000	0.001
import_qiime	0.754	0.011	0.766
import_qiime_otu_tax	0.688	0.060	0.751
import_qiime_sample_data	0.033	0.002	0.034
import_usearch_uc	0.020	0.004	0.023
index_reorder	0.000	0.000	0.001
intersect_taxa	0.000	0.000	0.001
make_network	3.920	0.088	4.038
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	1.115	0.188	1.306
merge_taxa-methods	0.075	0.003	0.079
microbio_me_qiime	0.779	0.019	0.845
mt-methods	2.077	0.030	2.152
nodeplotblank	0.419	0.003	0.425
nodeplotboot	0.003	0.000	0.002
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.033	0.001	0.035
ntaxa-methods	0.005	0.001	0.006
ordinate	0.001	0.000	0.001
otu_table-methods	0.001	0.000	0.001
parseTaxonomy-functions	0.003	0.000	0.003
phy_tree-methods	0.226	0.011	0.237
phyloseq	0.031	0.004	0.035
phyloseq_to_deseq2	0.445	0.057	0.526
plot_bar	2.621	0.117	2.774
plot_clusgap	4.328	0.138	4.584
plot_heatmap	4.972	0.220	5.367
plot_net	5.330	0.161	5.599
plot_network	2.971	0.043	3.050
plot_ordination	0.866	0.065	0.937
plot_phyloseq-methods	0.316	0.007	0.323
plot_richness	5.255	0.514	5.785
plot_scree	2.117	0.082	2.212
plot_tree	0.765	0.005	0.771
prune_samples-methods	0.702	0.101	0.804
prune_taxa-methods	0.050	0.005	0.055
psmelt	1.077	0.117	1.195
rank_names	0.029	0.008	0.036
rarefy_even_depth	0.118	0.006	0.125
read_tree	0.167	0.002	0.170
read_tree_greengenes	0.052	0.001	0.053
reconcile_categories	0.001	0.000	0.001
refseq-methods	0.237	0.019	0.256
rm_outlierf	0.021	0.001	0.022
sample_data-methods	0.060	0.010	0.071
sample_names-methods	0.003	0.008	0.011
sample_sums	0.034	0.018	0.052
sample_variables	0.028	0.009	0.036
show-methods	0.000	0.000	0.001
splat.phyloseq.objects	0	0	0
subset_ord_plot	0	0	0
subset_samples-methods	0	0	0
subset_taxa-methods	0.001	0.000	0.001
tax_glom	0.001	0.000	0.001
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.033	0.008	0.041
taxa_sums	0.039	0.022	0.061
threshrank	3.766	1.078	4.855
threshrankfun	0.077	0.003	0.080
tip_glom	0.954	0.008	0.989
topf	0.022	0.000	0.022
topk	0.021	0.000	0.021
topp	0.021	0.001	0.022
transformcounts	0.154	0.002	0.159
transpose-methods	1.020	0.636	1.659
tree_layout	0.733	0.008	0.756