BioC 2.14: CHECK report for phyloseq on morelia

Package: phyloseq

Version: 1.8.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.8.2.tar.gz

StartedAt: 2014-10-08 00:40:09 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:48:33 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 504.0 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/phyloseq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.8.2’
* 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 ... [29s/43s] 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘JSD.pair’ ‘UFwi’ ‘internal2tips_self’ ‘ufnum’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
JSD: no visible binding for global variable ‘i’
fastUniFrac: 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_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 ‘type’
plot_tree_only: no visible binding for global variable ‘type’
plot_tree_only: no visible binding for global variable ‘x’
plot_tree_only: no visible binding for global variable ‘y’
plot_tree_only: no visible binding for global variable ‘xend’
plot_tree_only: no visible binding for global variable ‘yend’
plot_tree_sampledodge: no visible binding for global variable ‘type’
plot_tree_sampledodge: no visible binding for global variable ‘value’
plot_tree_sampledodge: no visible binding for global variable ‘x’
plot_tree_sampledodge: no visible binding for global variable ‘x.adj’
plot_tree_sampledodge: no visible binding for global variable ‘y’
plot_tree_sampledodge: no visible binding for global variable
  ‘tipLabels’
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 ... NOTE
  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.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [94s/101s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plot_heatmap  5.776  0.235   6.199
nodeplotblank 4.767  0.047   5.739
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [78s/82s]
 [78s/82s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	4.013	0.174	4.318
JSD	0.001	0.000	0.001
UniFrac-methods	2.423	0.034	2.472
access	0.001	0.000	0.001
assign-otu_table	0.001	0.000	0.001
assign-phy_tree	0.043	0.004	0.047
assign-sample_data	0.829	0.023	0.880
assign-sample_names	0.011	0.005	0.016
assign-tax_table	0.001	0.000	0.001
assign-taxa_are_rows	0.003	0.005	0.008
assign-taxa_names	0.011	0.006	0.017
build_tax_table	0.018	0.001	0.018
capscale-phyloseq-methods	1.229	0.067	2.136
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	2.057	0.077	2.139
data-enterotype	2.497	0.020	2.621
data-esophagus	1.563	0.009	1.615
data-soilrep	2.229	0.146	2.410
distance	1.754	0.067	3.786
envHash2otu_table	0.001	0.000	0.001
estimate_richness	0.030	0.004	0.034
export_env_file	0	0	0
export_mothur_dist	0.073	0.018	0.091
extract-methods	0.012	0.003	0.016
filter_taxa	0.558	0.026	0.585
filterfun_sample	0.025	0.001	0.026
gapstat_ord	2.644	0.050	2.697
genefilter_sample-methods	0.001	0.000	0.001
get.component.classes	0.000	0.000	0.001
get_sample-methods	0.004	0.005	0.009
get_taxa-methods	0.004	0.004	0.008
get_taxa_unique	0.262	0.023	0.284
get_variable	0.224	0.012	0.235
getslots.phyloseq	0.203	0.016	0.220
import	0.000	0.000	0.001
import_RDP_otu	1.586	0.026	1.614
import_biom	0.192	0.002	0.214
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	0.543	0.006	0.550
import_qiime_otu_tax	0.518	0.048	0.567
import_qiime_sample_data	0.025	0.002	0.027
import_usearch_uc	0.021	0.004	0.049
index_reorder	0.001	0.000	0.001
intersect_taxa	0.001	0.000	0.001
make_network	4.619	0.080	4.763
merge_phyloseq	0.001	0.000	0.001
merge_phyloseq_pair-methods	0.002	0.001	0.002
merge_samples-methods	1.551	0.161	1.718
merge_taxa-methods	0.058	0.002	0.062
microbio_me_qiime	0.709	0.019	0.839
mt-methods	0.001	0.000	0.001
nodeplotblank	4.767	0.047	5.739
nodeplotboot	0.001	0.000	0.001
nodeplotdefault	0.001	0.000	0.001
nsamples-methods	0.015	0.003	0.029
ntaxa-methods	0.003	0.004	0.007
ordinate	0	0	0
otu_table-methods	0.000	0.001	0.001
parseTaxonomy-functions	0.002	0.000	0.009
phy_tree-methods	0.161	0.011	0.175
phyloseq	0.016	0.006	0.041
phyloseq_to_deseq2	0.912	0.043	0.961
plot_bar	2.574	0.107	2.812
plot_clusgap	4.536	0.121	4.696
plot_heatmap	5.776	0.235	6.199
plot_network	3.105	0.026	3.134
plot_ordination	1.302	0.073	1.376
plot_phyloseq-methods	3.235	0.025	3.262
plot_richness	4.375	0.358	4.823
plot_scree	2.121	0.067	2.196
plot_tree	2.464	0.022	3.279
prune_samples-methods	0.779	0.087	0.867
prune_taxa-methods	0.037	0.001	0.060
psmelt	1.088	0.098	1.212
rank_names	0.026	0.003	0.030
rarefy_even_depth	0.097	0.002	0.099
read_tree	0.137	0.004	0.141
read_tree_greengenes	0.053	0.001	0.068
reconcile_categories	0.001	0.000	0.000
refseq-methods	0.231	0.012	0.244
rm_outlierf	0.033	0.002	0.035
sample_data-methods	0.051	0.005	0.056
sample_names-methods	0.003	0.003	0.006
sample_sums	0.031	0.007	0.038
sample_variables	0.025	0.004	0.029
show-methods	0	0	0
splat.phyloseq.objects	0.001	0.000	0.001
subset_ord_plot	0.001	0.000	0.000
subset_samples-methods	0	0	0
subset_taxa-methods	0.000	0.000	0.001
tax_glom	0.001	0.000	0.001
tax_table-methods	0.001	0.000	0.000
taxa_names-methods	0.030	0.003	0.034
taxa_sums	0.041	0.012	0.053
threshrank	3.195	0.963	4.354
threshrankfun	0.062	0.004	0.066
tip_glom	2.042	0.006	2.051
topf	0.022	0.000	0.023
topk	0.022	0.001	0.022
topp	0.022	0.000	0.023
transformcounts	0.128	0.002	0.131
transpose-methods	0.895	0.579	1.684
tree.get.tags	0.001	0.000	0.001
tree.has.tags	0.001	0.000	0.000