BioC 2.14: CHECK report for phyloseq on zin2

Package: phyloseq

Version: 1.8.2

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.8.2.tar.gz

StartedAt: 2014-10-08 01:46:46 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:53:21 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 394.5 seconds

RetCode: 0

Status:  OK

CheckDir: phyloseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings phyloseq_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/phyloseq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.8.2’
* 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 ... [24s/24s] 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 ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
nodeplotblank 5.364  0.008   5.400
plot_heatmap  5.200  0.016   5.225
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘testthat-phyloseq.R’ [66s/66s]
 [66s/67s] 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
  ‘/home/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	3.344	0.016	3.373
JSD	0.000	0.000	0.001
UniFrac-methods	1.788	0.012	1.800
access	0.000	0.000	0.001
assign-otu_table	0.004	0.000	0.001
assign-phy_tree	0.036	0.000	0.036
assign-sample_data	0.745	0.008	0.751
assign-sample_names	0.008	0.000	0.008
assign-tax_table	0.000	0.000	0.001
assign-taxa_are_rows	0.000	0.000	0.003
assign-taxa_names	0.004	0.000	0.008
build_tax_table	0.012	0.000	0.012
capscale-phyloseq-methods	1.216	0.012	1.231
cca-rda-phyloseq-methods	0	0	0
data-GlobalPatterns	1.800	0.016	1.818
data-enterotype	2.380	0.000	2.385
data-esophagus	1.304	0.000	1.308
data-soilrep	1.940	0.012	1.953
distance	1.416	0.040	1.753
envHash2otu_table	0.004	0.000	0.000
estimate_richness	0.020	0.008	0.030
export_env_file	0	0	0
export_mothur_dist	0.060	0.016	0.077
extract-methods	0.008	0.000	0.011
filter_taxa	0.488	0.040	0.532
filterfun_sample	0.020	0.000	0.021
gapstat_ord	1.876	0.012	1.890
genefilter_sample-methods	0.004	0.000	0.000
get.component.classes	0	0	0
get_sample-methods	0.004	0.000	0.004
get_taxa-methods	0.004	0.000	0.003
get_taxa_unique	0.224	0.016	0.241
get_variable	0.184	0.004	0.186
getslots.phyloseq	0.172	0.000	0.172
import	0	0	0
import_RDP_otu	1.212	0.000	1.213
import_biom	0.160	0.000	0.161
import_env_file	0.000	0.000	0.001
import_mothur	0.000	0.000	0.001
import_mothur_dist	0.000	0.000	0.001
import_pyrotagger_tab	0	0	0
import_qiime	0.548	0.000	0.550
import_qiime_otu_tax	0.444	0.020	0.463
import_qiime_sample_data	0.020	0.000	0.021
import_usearch_uc	0.016	0.000	0.017
index_reorder	0.000	0.000	0.001
intersect_taxa	0.004	0.000	0.000
make_network	4.301	0.004	4.337
merge_phyloseq	0.000	0.000	0.001
merge_phyloseq_pair-methods	0.000	0.000	0.001
merge_samples-methods	1.356	0.024	1.383
merge_taxa-methods	0.052	0.000	0.049
microbio_me_qiime	0.588	0.036	0.639
mt-methods	0	0	0
nodeplotblank	5.364	0.008	5.400
nodeplotboot	0.000	0.000	0.002
nodeplotdefault	0.000	0.000	0.001
nsamples-methods	0.020	0.000	0.019
ntaxa-methods	0.004	0.000	0.003
ordinate	0.000	0.000	0.001
otu_table-methods	0	0	0
parseTaxonomy-functions	0.000	0.000	0.002
phy_tree-methods	0.164	0.008	0.174
phyloseq	0.020	0.000	0.019
phyloseq_to_deseq2	0.988	0.036	1.024
plot_bar	2.256	0.020	2.280
plot_clusgap	4.517	0.040	4.581
plot_heatmap	5.200	0.016	5.225
plot_network	2.980	0.004	2.993
plot_ordination	0.904	0.008	0.915
plot_phyloseq-methods	2.768	0.000	2.773
plot_richness	3.969	0.008	3.985
plot_scree	1.848	0.004	1.861
plot_tree	3.068	0.000	3.071
prune_samples-methods	0.664	0.004	0.667
prune_taxa-methods	0.028	0.000	0.030
psmelt	1.000	0.004	1.008
rank_names	0.024	0.000	0.024
rarefy_even_depth	0.080	0.000	0.082
read_tree	0.128	0.000	0.129
read_tree_greengenes	0.044	0.000	0.073
reconcile_categories	0.000	0.000	0.001
refseq-methods	0.168	0.004	0.169
rm_outlierf	0.016	0.000	0.016
sample_data-methods	0.044	0.004	0.050
sample_names-methods	0.000	0.000	0.002
sample_sums	0.024	0.004	0.029
sample_variables	0.024	0.000	0.023
show-methods	0	0	0
splat.phyloseq.objects	0.000	0.000	0.001
subset_ord_plot	0	0	0
subset_samples-methods	0.000	0.000	0.001
subset_taxa-methods	0	0	0
tax_glom	0.000	0.000	0.001
tax_table-methods	0.000	0.000	0.001
taxa_names-methods	0.020	0.004	0.023
taxa_sums	0.032	0.000	0.033
threshrank	2.268	0.516	2.790
threshrankfun	0.048	0.000	0.049
tip_glom	1.724	0.004	1.731
topf	0.016	0.000	0.016
topk	0.012	0.000	0.016
topp	0.016	0.000	0.016
transformcounts	0.100	0.000	0.099
transpose-methods	1.016	0.300	1.317
tree.get.tags	0.000	0.000	0.001
tree.has.tags	0	0	0