BioC 3.1: CHECK report for phyloseq on petty

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 01:05:35 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:15:17 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 581.3 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [33s/33s] 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
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’
JSD: no visible binding for global variable ‘i’
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 ... [113s/116s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_richness 6.818  0.687   7.512
plot_heatmap  6.801  0.401   7.215
plot_net      6.876  0.181   7.069
DPCoA         6.020  0.253   6.278
plot_clusgap  5.961  0.200   6.185
threshrank    4.073  1.584   5.663
make_network  5.299  0.133   5.451
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [121s/122s]
 [122s/122s] 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	6.020	0.253	6.278
JSD	0.001	0.000	0.001
UniFrac-methods	0.245	0.008	0.253
access	0.001	0.000	0.002
assign-otu_table	0.002	0.000	0.002
assign-phy_tree	0.086	0.005	0.092
assign-sample_data	0.813	0.043	0.856
assign-sample_names	0.014	0.003	0.018
assign-tax_table	0.001	0.000	0.003
assign-taxa_are_rows	0.005	0.004	0.009
assign-taxa_names	0.015	0.004	0.020
build_tax_table	0.024	0.001	0.025
capscale-phyloseq-methods	1.769	0.118	1.890
cca-rda-phyloseq-methods	0.001	0.000	0.001
data-GlobalPatterns	2.143	0.119	2.265
data-enterotype	2.805	0.037	2.846
data-esophagus	1.144	0.016	1.163
data-soilrep	2.153	0.185	2.339
distance	0.319	0.057	2.674
envHash2otu_table	0.002	0.000	0.002
estimate_richness	0.047	0.005	0.054
export_env_file	0.001	0.000	0.001
export_mothur_dist	0.188	0.034	0.222
extract-methods	0.016	0.006	0.022
filter_taxa	0.813	0.039	0.852
filterfun_sample	0.031	0.000	0.031
gapstat_ord	3.345	0.064	3.477
genefilter_sample-methods	0.001	0.000	0.002
get.component.classes	0.000	0.000	0.001
get_sample-methods	0.006	0.004	0.009
get_taxa-methods	0.006	0.003	0.010
get_taxa_unique	0.444	0.033	0.478
get_variable	0.303	0.014	0.318
getslots.phyloseq	0.352	0.028	0.380
import	0.001	0.000	0.001
import_RDP_otu	1.556	0.030	1.586
import_biom	0.289	0.015	0.327
import_env_file	0.001	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	1.140	0.005	1.147
import_qiime_otu_tax	0.938	0.059	1.001
import_qiime_sample_data	0.025	0.001	0.026
import_usearch_uc	0.020	0.006	0.025
index_reorder	0.001	0.000	0.000
intersect_taxa	0.001	0.001	0.001
make_network	5.299	0.133	5.451
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.002	0.000	0.003
merge_samples-methods	1.393	0.287	1.680
merge_taxa-methods	0.094	0.004	0.098
microbio_me_qiime	1.033	0.039	1.297
mt-methods	2.945	0.040	2.988
nodeplotblank	0.566	0.006	0.574
nodeplotboot	0.004	0.001	0.004
nodeplotdefault	0.001	0.000	0.002
nsamples-methods	0.050	0.003	0.053
ntaxa-methods	0.006	0.004	0.009
ordinate	0.001	0.000	0.001
otu_table-methods	0.001	0.000	0.002
parseTaxonomy-functions	0.005	0.000	0.005
phy_tree-methods	0.241	0.019	0.264
phyloseq	0.043	0.008	0.051
phyloseq_to_deseq2	0.946	0.110	1.055
plot_bar	3.053	0.178	3.235
plot_clusgap	5.961	0.200	6.185
plot_heatmap	6.801	0.401	7.215
plot_net	6.876	0.181	7.069
plot_network	4.012	0.048	4.068
plot_ordination	1.277	0.111	1.390
plot_phyloseq-methods	0.444	0.009	0.464
plot_richness	6.818	0.687	7.512
plot_scree	2.583	0.105	2.692
plot_tree	1.026	0.007	1.037
prune_samples-methods	1.024	0.166	1.191
prune_taxa-methods	0.062	0.004	0.066
psmelt	1.579	0.202	1.785
rank_names	0.038	0.008	0.049
rarefy_even_depth	0.188	0.006	0.194
read_tree	0.248	0.002	0.250
read_tree_greengenes	0.074	0.001	0.075
reconcile_categories	0.001	0.000	0.000
refseq-methods	0.234	0.019	0.254
rm_outlierf	0.026	0.001	0.027
sample_data-methods	0.103	0.016	0.119
sample_names-methods	0.004	0.008	0.012
sample_sums	0.050	0.022	0.071
sample_variables	0.034	0.009	0.043
show-methods	0.001	0.000	0.000
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0.000	0.000	0.001
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.001	0.000
tax_glom	0.002	0.000	0.002
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.049	0.009	0.058
taxa_sums	0.055	0.023	0.079
threshrank	4.073	1.584	5.663
threshrankfun	0.094	0.004	0.098
tip_glom	1.327	0.007	1.409
topf	0.045	0.001	0.045
topk	0.028	0.001	0.029
topp	0.030	0.001	0.032
transformcounts	0.208	0.004	0.255
transpose-methods	1.463	0.930	2.445
tree_layout	1.024	0.028	1.064