BioC 3.1: CHECK report for phyloseq on morelia

Package: phyloseq

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings phyloseq_1.12.2.tar.gz

StartedAt: 2015-10-09 04:51:08 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:57:25 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 376.9 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_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.12.2’
* 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 ... [21s/22s] 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 ... [71s/73s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [78s/78s]
 [78s/78s] 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-3.1-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.
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** 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.
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (phyloseq)

name	user	system	elapsed
DPCoA	3.713	0.346	4.070
JSD	0.001	0.000	0.001
UniFrac-methods	0.155	0.020	0.174
access	0.001	0.000	0.001
assign-otu_table	0.002	0.001	0.002
assign-phy_tree	0.052	0.025	0.078
assign-sample_data	0.152	0.028	0.179
assign-sample_names	0.006	0.006	0.012
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.002	0.006	0.008
assign-taxa_names	0.009	0.008	0.016
build_tax_table	0.015	0.001	0.016
capscale-phyloseq-methods	0.870	0.090	0.961
cca-rda-phyloseq-methods	0.001	0.000	0.001
data-GlobalPatterns	1.672	0.081	1.753
data-enterotype	1.805	0.029	1.835
data-esophagus	0.572	0.009	0.582
data-soilrep	1.696	0.276	1.975
distance	0.221	0.038	2.359
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.027	0.002	0.029
export_env_file	0.001	0.000	0.000
export_mothur_dist	0.110	0.020	0.129
extract-methods	0.012	0.002	0.013
filter_taxa	0.181	0.014	0.194
filterfun_sample	0.016	0.001	0.017
gapstat_ord	2.187	0.117	2.306
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.001	0.000	0.000
get_sample-methods	0.002	0.004	0.007
get_taxa-methods	0.004	0.004	0.008
get_taxa_unique	0.243	0.025	0.268
get_variable	0.178	0.015	0.193
getslots.phyloseq	0.198	0.020	0.219
import	0	0	0
import_RDP_otu	1.145	0.056	1.201
import_biom	0.172	0.007	0.205
import_env_file	0.000	0.001	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	0.657	0.014	0.671
import_qiime_otu_tax	0.506	0.050	0.578
import_qiime_sample_data	0.027	0.001	0.027
import_usearch_uc	0.020	0.005	0.024
index_reorder	0.001	0.000	0.000
intersect_taxa	0.001	0.000	0.001
make_network	3.081	0.176	3.259
merge_phyloseq	0.001	0.001	0.001
merge_phyloseq_pair-methods	0.001	0.000	0.001
merge_samples-methods	0.951	0.186	1.137
merge_taxa-methods	0.068	0.005	0.073
microbio_me_qiime	0.599	0.110	0.751
mt-methods	1.354	0.074	1.429
nodeplotblank	0.382	0.023	0.405
nodeplotboot	0.002	0.000	0.001
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.026	0.006	0.032
ntaxa-methods	0.004	0.008	0.013
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	0.162	0.039	0.202
phyloseq	0.027	0.007	0.033
phyloseq_to_deseq2	0.668	0.062	0.731
plot_bar	1.793	0.109	1.905
plot_clusgap	3.810	0.259	4.106
plot_heatmap	3.741	0.388	4.132
plot_net	4.498	0.215	4.726
plot_network	2.503	0.239	2.773
plot_ordination	0.724	0.063	0.789
plot_phyloseq-methods	0.302	0.009	0.313
plot_richness	4.381	0.497	4.886
plot_scree	1.678	0.120	1.827
plot_tree	0.533	0.034	0.568
prune_samples-methods	0.581	0.123	0.703
prune_taxa-methods	0.035	0.009	0.045
psmelt	1.258	0.217	1.477
rank_names	0.028	0.012	0.040
rarefy_even_depth	0.087	0.011	0.097
read_tree	0.099	0.003	0.103
read_tree_greengenes	0.037	0.008	0.045
reconcile_categories	0	0	0
refseq-methods	0.181	0.040	0.221
rm_outlierf	0.013	0.001	0.014
sample_data-methods	0.049	0.029	0.078
sample_names-methods	0.002	0.015	0.018
sample_sums	0.029	0.025	0.054
sample_variables	0.026	0.012	0.039
show-methods	0.001	0.001	0.001
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	0	0
tax_glom	0.001	0.001	0.001
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.031	0.012	0.044
taxa_sums	0.037	0.032	0.070
threshrank	2.203	0.947	3.154
threshrankfun	0.049	0.004	0.054
tip_glom	0.858	0.066	0.925
topf	0.016	0.000	0.016
topk	0.012	0.000	0.012
topp	0.017	0.002	0.020
transformcounts	0.125	0.005	0.130
transpose-methods	0.823	0.570	1.393
tree_layout	0.607	0.029	0.671